[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Prefix of PLINK files, i.e. path/2/name.bed, path/2/name.bim and path/2/name.fam.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] prefix of plink files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory where prefixMergedDataset.eigenvec results as returned by plink –pca should be saved. Per default qcdir=indir. If run.check_ancestry is FALSE, it is assumed that plink –pca prefixMergedDataset has been run and qcdir/prefixMergedDataset.eigenvec exists.User needs writing permission to qcdir.

[character] Prefix of merged dataset (study and reference samples) used in plink –pca, resulting in prefixMergedDataset.eigenvec.

[double] Scaling factor of radius to be drawn around center of European reference samples, with study samples inside this radius considered to be of European descent and samples outside this radius of non-European descent. The radius is computed as the maximum Euclidean distance of European reference samples to the centre of European reference samples.

[character] Option to use pre-downloaded individual and population identifiers from either the 1000Genomes or HapMap project. If refSamples and refSamplesFile are not provided, the HapMap identifiers (or 1000Genomes is specified) will be used as default and the function will fail if the reference samples in the prefixMergedDataset do not match these reference samples. If refColors and refColorsFile are not provided, this also sets default colors for the reference populations.

[vector] Vector with population identifiers of European reference population. Identifiers have to be corresponding to population IDs [refColorsPop] in refColorsfile/refColors.

[data.frame] Dataframe with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors. Either refSamples or refSamplesFile have to be specified.

[data.frame, optional] Dataframe with population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor]. If not provided and is.null(refColorsFile) default colors are used.

[character] /path/to/File/with/reference samples. Needs columns with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors.

[character, optional] /path/to/File/with/Population/Colors containing population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor].If not provided and is.null(refColors) default colors for are used.

[character] Column name of reference sample IDs in refSamples/refSamplesFile.

[character] Column name of reference sample population IDs in refSamples/refSamplesFile.

[character] Column name of population colors in refColors/refColorsFile

[character] Column name of reference sample population IDs in refColors/refColorsFile.

[character] Colour to be used for study population.

[integer] Number of population names per row in PCA plot.

[logical] Should plink –pca be run to determine principal components of merged dataset; if FALSE, it is assumed that plink –pca has been run successfully and qcdir/prefixMergedDataset.eigenvec is present; check_ancestry will fail with missing file error otherwise.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_ancestry) via ggplot2::ggsave(p=p_ancestry, other_arguments) or pdf(outfile) print(p_ancestry) dev.off().

[logical] If TRUE, progress info is printed to standard out.

[character vector] Vector of sample IIDs to highlight in the plot (p_ancestry); all highlight_samples IIDs have to be present in the IIDs of the prefixMergedDataset.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified.Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam, name.het and name.imiss.

[character] /path/to/directory where name.het as returned by plink –het and name.imiss as returned by plink –missing will be saved. Per default qcdir=indir. If run.check_het_and_miss is FALSE, it is assumed that plink –missing and plink –het have been run and qcdir/name.imiss and qcdir/name.het are present. User needs writing permission to qcdir.

[double] Threshold for acceptable missing genotype rate per individual; has to be proportion between (0,1)

[double] Threshold for acceptable deviation from mean heterozygosity per individual. Expressed as multiples of standard deviation of heterozygosity (het), i.e. individuals outside mean(het) +/- hetTh*sd(het) will be returned as failing heterozygosity check; has to be larger than 0.

[logical] Should plink –missing and plink –het be run to determine genotype missingness and heterozygosity rates; if FALSE, it is assumed that plink –missing and plink –het have been run and qcdir/name.imiss and qcdir/name.het are present; check_het_and_miss will fail with missing file error otherwise.

[logical] Set TRUE, to add fail IDs as text labels in scatter plot.

[character vector] Vector of sample IIDs to highlight in the plot (p_het_imiss); all highlight_samples IIDs have to be present in the IIDs of the name.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified.Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_het_imiss) via ggplot2::ggsave(p=p_het_imiss , other_arguments) or pdf(outfile) print(p_het_imiss) dev.off().

[logical] If TRUE, progress info is printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory where results will be written to. If perIndividualQC was conducted, this directory should be the same as qcdir specified in perIndividualQC, i.e. it contains name.fail.IDs with IIDs of individuals that failed QC. User needs writing permission to qcdir. Per default, qcdir=indir.

[double] Significance threshold for deviation from HWE.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_hwe) via ggplot2::ggsave(p=p_hwe, other_arguments) or pdf(outfile) print(p_hwe) dev.off().

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, progress info is printed to standard out and specifically, if TRUE, plink log will be displayed.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory where results will be written to. If perIndividualQC was conducted, this directory should be the same as qcdir specified in perIndividualQC, i.e. it contains name.fail.IDs with IIDs of individuals that failed QC. User needs writing permission to qcdir. Per default, qcdir=indir.

[double] Threshold for minor allele cut cut-off, if both mafTh and macTh are specified, macTh is used (macTh = mafTh\*2\*NrSamples).

[double] Threshold for minor allele frequency cut-off.

[logical] If TRUE, progress info is printed to standard out and specifically, if TRUE, plink log will be displayed.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_hwe) via ggplot2::ggsave(p=p_maf, other_arguments) or pdf(outfile) print(p_maf) dev.off().

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam, name.genome and name.imiss.

[character] /path/to/directory to where name.genome as returned by plink –genome will be saved. Per default qcdir=indir. If run.check_relatedness is FALSE, it is assumed that plink –missing and plink –genome have been run and qcdir/name.imiss and qcdir/name.genome exist. User needs writing permission to qcdir.

[double] Threshold for acceptable proportion of IBD between pair of individuals.

[logical] Should high LD regions be filtered before IBD estimation; carried out per default with high LD regions for hg19 provided as default via genomebuild. For alternative genome builds not provided or non-human data, high LD regions files can be provided via high_ldregion_file.

[character] Path to file with high LD regions used for filtering before IBD estimation if filter_high_ldregion == TRUE, otherwise ignored; for human genome data, high LD region files are provided and can simply be chosen via genomebuild. Files have to be space-delimited, no column names with the following columns: chromosome, region-start, region-end, region number. Chromosomes are specified without 'chr' prefix. For instance: 1 48000000 52000000 1 2 86000000 100500000 2

[character] Name of the genome build of the PLINK file annotations, ie mappings in the name.bim file. Will be used to remove high-LD regions based on the coordinates of the respective build. Options are hg18, hg19 and hg38. See @details.

[double] Threshold for acceptable missing genotype rate in any individual; has to be proportion between (0,1)

[logical] Should plink –genome be run to determine pairwise IBD of individuals; if FALSE, it is assumed that plink –genome and plink –missing have been run and qcdir/name.imiss and qcdir/name.genome are present; check_relatedness will fail with missing file error otherwise.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_IBD() via ggplot2::ggsave(p=p_IBD, other_arguments) or pdf(outfile) print(p_IBD) dev.off().

[logical] If TRUE, progress info is printed to standard out.

[double] Threshold of minor allele frequency filter for selecting variants for IBD estimation.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam and name.sexcheck.

[character] /path/to/directory to save name.sexcheck as returned by plink –check-sex. Per default qcdir=indir. If run.check_sex is FALSE, it is assumed that plink –check-sex has been run and qcdir/name.sexcheck is present. User needs writing permission to qcdir.

[double] Threshold of X-chromosomal heterozygosity rate for males.

[double] Threshold of X-chromosomal heterozygosity rate for females.

[logical] Should plink –check-sex be run? if set to FALSE, it is assumed that plink –check-sex has been run and qcdir/name.sexcheck is present; check_sex will fail with missing file error otherwise.

[data.frame, optional] Dataframe with sample IDs [externalSexID] and sex [externalSexSex] to double check if external and PEDSEX data (often processed at different centers) match.

[integer/character] Identifier for 'female' in externalSex.

[integer/character] Identifier for 'male' in externalSex.

[character] Column identifier for column containing sex information in externalSex.

[character] Column identifier for column containing ID information in externalSex.

[logical] Should PEDSEX of individuals with mismatch between PEDSEX and Sex while Sex==SNPSEX automatically corrected: this will directly change the name.bim/.bed/.fam files!

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_sexcheck) via ggplot2::ggsave(p=p_sexcheck, other_arguments) or pdf(outfile) print(p_sexcheck) dev.off().

[logical] If TRUE, progress info is printed to standard out.

[logical] Set TRUE, to add fail IDs as text labels in scatter plot.

[character vector] Vector of sample IIDs to highlight in the plot (p_sexcheck); all highlight_samples IIDs have to be present in the IIDs of the name.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified. Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory where results will be written to. If perIndividualQC was conducted, this directory should be the same as qcdir specified in perIndividualQC, i.e. it contains name.fail.IDs with IIDs of individuals that failed QC. User needs writing permission to qcdir. Per default, qcdir=indir.

[double] Threshold for acceptable variant missing rate across samples.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_lmiss) via ggplot2::ggsave(p=p_lmiss, other_arguments) or pdf(outfile) print(p_lmiss) dev.off().

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, progress info is printed to standard out and specifically, if TRUE, plink log will be displayed.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory where results will be written to. If perIndividualQC was conducted, this directory should be the same as qcdir specified in perIndividualQC, i.e. it contains name.fail.IDs with IIDs of individuals that failed QC. User needs writing permission to qcdir. Per default, qcdir=indir.

[logical] Set to exclude samples that failed the sex check (via check_sex or perIndividualQC). Requires file qcdir/name.fail-sexcheck.IDs (automatically created by perIndividualQC if do.evaluate_check_sex set to TRUE).

[logical] Set to exclude samples that failed check for outlying heterozygosity rates (via check_het_and_miss or perIndividualQC). Requires file qcdir/name.fail-het.IDs (automatically created by perIndividualQC if do.evaluate_check_het_and_miss set to TRUE).

[logical] Set to exclude samples that failed check for excessive missing genotype rates (via check_het_and_miss or perIndividualQC). Requires file qcdir/name.fail-imiss.IDs (automatically created by perIndividualQC if do.evaluate_check_het_and_miss set to TRUE).

[logical] Set to exclude samples that failed ancestry check (via check_ancestry or perIndividualQC). Requires file qcdir/name.fail-ancestry.IDs (automatically created by perIndividualQC if do.check_ancestry set to TRUE).

[logical] Set to exclude samples that failed relatedness check (via check_relatedness or perIndividualQC). Requires file qcdir/name.fail-IBD.IDs (automatically created by perIndividualQC if do.evaluate_check_relatedness set to TRUE).

[logical] Set to exclude markers that have excessive missing rates across samples (via check_snp_missingness or perMarkerQC). Requires lmissTh to be set.

[double] Threshold for acceptable variant missing rate across samples.

[logical] Set to exclude markers that fail HWE exact test (via check_hwe or perMarkerQC). Requires hweTh to be set.

[double] Significance threshold for deviation from HWE.

[logical] Set to exclude markers that fail minor allele frequency or minor allele count threshold (via check_maf or perMarkerQC). Requires mafTh or macTh to be set.

[double] Threshold for minor allele cut cut-off, if both mafTh and macTh are specified, macTh is used (macTh = mafTh\*2\*NrSamples).

[double] Threshold for minor allele frequency cut-off.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, progress info is printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] Prefix of merged dataset (study and reference samples) used in plink –pca, resulting in prefixMergedDataset.eigenvec.

[character] /path/to/directory/with/QC/results containing prefixMergedDataset.eigenvec results as returned by plink –pca. Per default qcdir=indir.

[double] Scaling factor of radius to be drawn around center of European reference samples, with study samples inside this radius considered to be of European descent and samples outside this radius of non-European descent. The radius is computed as the maximum Euclidean distance of European reference samples to the centre of European reference samples.

[character] Option to use pre-downloaded individual and population identifiers from either the 1000Genomes or HapMap project. If refSamples and refSamplesFile are not provided, the HapMap identifiers (or 1000Genomes is specified) will be used as default and the function will fail if the reference samples in the prefixMergedDataset do not match these reference samples. If refColors and refColorsFile are not provided, this also sets default colors for the reference populations.

[data.frame] Dataframe with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors. If refSamples and refSamplesFile are not specified, defaultRefSamples will be used as reference.

[data.frame, optional] Dataframe with population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor]. If refColors and refColorsFile are not specified and refSamples and refSamplesFile are not specified, default colors will be determined from the defaultRefSamples option. If refColors and refColorsFile are not specified and but refSamples or refSamplesFile are given, ggplot default colors will be used.

[character] /path/to/File/with/reference samples. Needs columns with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors. If both refSamplesFile and refSamples are not NULL, defaultRefSamples information is used.

[character, optional] /path/to/File/with/Population/Colors containing population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor]. If refColors and refColorsFile are not specified and refSamples and refSamplesFile are not specified, default colors will be determined from the defaultRefSamples option. If refColors and refColorsFile are not specified and but refSamples or refSamplesFile are given, ggplot default colors will be used.

[character] Column name of reference sample IDs in refSamples/refSamplesFile.

[character] Column name of reference sample population IDs in refSamples/refSamplesFile.

[character] Column name of population colors in refColors/refColorsFile

[character] Column name of reference sample population IDs in refColors/refColorsFile.

[character] Colour to be used for study population if plot is TRUE.

[vector] Vector with population identifiers of European reference population. Identifiers have to be corresponding to population IDs [refColorsPop] in refColorsfile/refColors.

[integer] Number of population names per row in PCA plot.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character vector] Vector of sample IIDs to highlight in the plot (p_ancestry); all highlight_samples IIDs have to be present in the IIDs of the prefixMergedDataset.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified.Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_ancestry) via ggplot2::ggsave(p=p_ancestry, other_arguments) or pdf(outfile) print(p_ancestry) dev.off().

[logical] If TRUE, progress info is printed to standard out.

[character] path/to/directory/with/QC/results containing name.imiss and name.het results as returned by plink –missing and plink –het.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam, name.het and name.imiss.

[double] Threshold for acceptable missing genotype rate in any individual; has to be proportion between (0,1)

[double] Threshold for acceptable deviation from mean heterozygosity in any individual. Expressed as multiples of standard deviation of heterozygosity (het), i.e. individuals outside mean(het) +/- hetTh*sd(het) will be returned as failing heterozygosity check; has to be larger than 0.

[logical] Set TRUE, to add fail IDs as text labels in scatter plot.

[character vector] Vector of sample IIDs to highlight in the plot (p_het_imiss); all highlight_samples IIDs have to be present in the IIDs of the name.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified.Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_het_imiss) via ggplot2::ggsave(p=p_het_imiss , other_arguments) or pdf(outfile) print(p_het_imiss) dev.off().

[character] path/to/directory/with/QC/results containing name.imiss and name.genome results as returned by plink –missing and plink –genome.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam, name.genome and name.imiss.

[double] Threshold for acceptable proportion of IBD between pair of individuals.

[double] Threshold for acceptable missing genotype rate in any individual; has to be proportion between (0,1)

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_IBD() via ggplot2::ggsave(p=p_IBD, other_arguments) or pdf(outfile) print(p_IBD) dev.off().

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[logical] If TRUE, progress info is printed to standard out.

[character] /path/to/directory containing name.sexcheck as returned by plink –check-sex.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam and name.sexcheck.

[double] Threshold of X-chromosomal heterozygosity rate for males.

[double] Threshold of X-chromosomal heterozygosity rate for females.

[data.frame, optional] with sample IDs [externalSexID] and sex [externalSexSex] to double check if external and PEDSEX data (often processed at different centers) match.

[logical] Should PEDSEX of individuals with mismatch between PEDSEX and Sex, with Sex==SNPSEX automatically corrected: this will directly change the name.bim/.bed/.fam files!

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files; only required of fixMixup==TRUE. User needs writing permission to indir.

[integer/character] Identifier for 'female' in externalSex.

[integer/character] Identifier for 'male' in externalSex.

[character] Column identifier for column containing sex information in externalSex.

[character] Column identifier for column containing ID information in externalSex.

[logical] If TRUE, progress info is printed to standard out.

[logical] Set TRUE, to add fail IDs as text labels in scatter plot.

[character vector] Vector of sample IIDs to highlight in the plot (p_sexcheck); all highlight_samples IIDs have to be present in the IIDs of the name.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified. Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, plink log and error messages are printed to standard out.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_sexcheck) via ggplot2::ggsave(p=p_sexcheck, other_arguments) or pdf(outfile) print(p_sexcheck) dev.off().

[list] Output of perIndividualQC i.e. named [list] with i) sample_missingness containing a [vector] with sample IIDs failing the selected missingness threshold imissTh, ii) highIBD containing a [vector] with sample IIDs failing the selected relatedness threshold highIBDTh, iii) outlying_heterozygosity containing a [vector] with sample IIDs failing selected the heterozygosity threshold hetTh, iv) mismatched_sex containing a [vector] with the sample IIDs failing the sexcheck based on SNPSEX and selected femaleTh/maleTh, v) ancestry containing a vector with sample IIDs failing the ancestry check based on the selected europeanTh and vi) p_sampleQC, a ggplot2-object 'containing' a sub-paneled plot with the QC-plots of check_sex, check_het_and_miss, check_relatedness and check_ancestry.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_overview) via ggplot2::ggsave(p=p_overview, other_arguments) or pdf(outfile) print(p_overview) dev.off().

[list] Output of perIndividualQC i.e. named [list] with i) fail_list, a named [list] with 1. SNP_missingness, containing SNP IDs failing the missingness threshold lmissTh, 2. hwe, containing SNP IDs failing the HWE exact test threshold hweTh and 3. maf, containing SNPs failing the MAF threshold mafTh/MAC threshold macTh and ii) p_markerQC, a ggplot2-object 'containing' a sub-paneled plot with the QC-plots of check_snp_missingness, check_hwe and check_maf

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_overview) via ggplot2::ggsave(p=p_overview, other_arguments) or pdf(outfile) print(p_overview) dev.off().

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory where results will be saved. Per default, qcdir=indir. If do.evaluate_[analysis] is set to TRUE and do.run_[analysis] is FALSE, perIndividualQC expects the analysis-specific plink output files in qcdir i.e. do.check_sex expects name.sexcheck, do.evaluate_check_het_and_miss expects name.het and name.imiss, do.evaluate_check_relatedness expects name.genome and name.imiss and do.evaluate_check_ancestry expects prefixMergeData.eigenvec. If these files are not present perIndividualQC will fail with missing file error. Setting do.run_[analysis] TRUE will execute the checks and create the required files. User needs writing permission to qcdir.

[logical] If TRUE, no sex check will be conducted; short for do.run_check_sex=FALSE and do.evaluate_check_sex=FALSE. Takes precedence over do.run_check_sex and do.evaluate_check_sex.

[logical] If TRUE, run run_check_sex

[logical] If TRUE, run evaluate_check_sex

[double] Threshold of X-chromosomal heterozygosity rate for males.

[double] Threshold of X-chromosomal heterozygosity rate for females.

[data.frame, optional] Dataframe with sample IDs [externalSexID] and sex [externalSexSex] to double check if external and PEDSEX data (often processed at different centers) match.

[integer/character] Identifier for 'male' in externalSex.

[character] Column identifier for column containing sex information in externalSex.

[character] Column identifier for column containing ID information in externalSex.

[integer/character] Identifier for 'female' in externalSex.

[logical] Should PEDSEX of individuals with mismatch between PEDSEX and Sex while Sex==SNPSEX automatically corrected: this will directly change the name.bim/.bed/.fam files!

[logical] If TRUE, no heterozygosity and missingness check will be conducted; short for do.run_check_heterozygosity=FALSE, do.run_check_missingness=FALSE and do.evaluate_check_het_and_miss=FALSE. Takes precedence over do.run_check_heterozygosity, do.run_check_missingness and do.evaluate_check_het_and_miss.

[logical] If TRUE, run run_check_heterozygosity and run_check_missingness

[logical] If TRUE, run evaluate_check_het_and_miss.

[double] Threshold for acceptable missing genotype rate in any individual; has to be proportion between (0,1)

[double] Threshold for acceptable deviation from mean heterozygosity per individual. Expressed as multiples of standard deviation of heterozygosity (het), i.e. individuals outside mean(het) +/- hetTh*sd(het) will be returned as failing heterozygosity check; has to be larger than 0.

[logical] If TRUE, no relatedness check will be conducted; short for do.run_check_relatedness=FALSE and do.evaluate_check_relatedness=FALSE. Takes precedence over do.run_check_relatedness and do.evaluate_check_relatedness.

[logical] If TRUE, run run_check_relatedness.

[logical] If TRUE, run evaluate_check_relatedness.

[double] Threshold for acceptable proportion of IBD between pair of individuals.

[double] Threshold of minor allele frequency filter for selecting variants for IBD estimation.

[logical] Should high LD regions be filtered before IBD estimation; carried out per default with high LD regions for hg19 provided as default via genomebuild. For alternative genome builds not provided or non-human data, high LD regions files can be provided via high_ldregion_file.

[character] Path to file with high LD regions used for filtering before IBD estimation if filter_high_ldregion == TRUE, otherwise ignored; for human genome data, high LD region files are provided and can simply be chosen via genomebuild. Files have to be space-delimited, no column names with the following columns: chromosome, region-start, region-end, region number. Chromosomes are specified without 'chr' prefix. For instance: 1 48000000 52000000 1 2 86000000 100500000 2

[character] Name of the genome build of the PLINK file annotations, ie mappings in the name.bim file. Will be used to remove high-LD regions based on the coordinates of the respective build. Options are hg18, hg19 and hg38. See @details.

[logical] If TRUE, no ancestry check will be conducted; short for do.run_check_ancestry=FALSE and do.evaluate_check_ancestry=FALSE. Takes precedence over do.run_check_ancestry and do.evaluate_check_ancestry.

[logical] If TRUE, run run_check_ancestry.

[logical] If TRUE, run evaluate_check_ancestry.

[character] Prefix of merged dataset (study and reference samples) used in plink –pca, resulting in prefixMergedDataset.eigenvec.

[double] Scaling factor of radius to be drawn around center of European reference samples, with study samples inside this radius considered to be of European descent and samples outside this radius of non-European descent. The radius is computed as the maximum Euclidean distance of European reference samples to the centre of European reference samples.

[character] Option to use pre-downloaded individual and population identifiers from either the 1000Genomes or HapMap project. If refSamples and refSamplesFile are not provided, the HapMap identifiers (or 1000Genomes is specified) will be used as default and the function will fail if the reference samples in the prefixMergedDataset do not match these reference samples. If refColors and refColorsFile are not provided, this also sets default colors for the reference populations.

[data.frame] Dataframe with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors. Either refSamples or refSamplesFile have to be specified.

[data.frame, optional] Dataframe with population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor]. If not provided and is.null(refColorsFile) default colors are used.

[character] /path/to/File/with/reference samples. Needs columns with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors.

[character, optional] /path/to/File/with/Population/Colors containing population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor].If not provided and is.null(refColors) default colors for are used.

[character] Column name of reference sample IDs in refSamples/refSamplesFile.

[character] Column name of reference sample population IDs in refSamples/refSamplesFile.

[character] Column name of population colors in refColors/refColorsFile

[character] Column name of reference sample population IDs in refColors/refColorsFile.

[character] Colour to be used for study population.

[logical] Set TRUE, to add fail IDs as text labels in scatter plot.

[character vector] Vector of sample IIDs to highlight in the plot (p_sexcheck); all highlight_samples IIDs have to be present in the IIDs of the name.fam file.

[character] Type of sample highlight, labeling by IID ("text"/"label") and/or highlighting data points in different "color" and/or "shape". "text" and "label" use ggrepel for minimal overlap of text labels ("text) or label boxes ("label"). Only one of "text" and "label" can be specified. Text/Label size can be specified with highlight_text_size, highlight color with highlight_color, or highlight shape with highlight_shape.

[integer] Text/Label size for samples specified to be highlighted (highlight_samples) by "text" or "label" (highlight_type).

[character] Color for samples specified to be highlighted (highlight_samples) by "color" (highlight_type).

[integer] Shape for samples specified to be highlighted (highlight_samples) by "shape" (highlight_type). Possible shapes and their encoding can be found at: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#sec:shape-spec

[logical] Should a separate legend for the highlighted samples be provided; only relevant for highlight_type == "color" or highlight_type == "shape".

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_sampleQC) via ggplot2::ggsave(p=p_sampleQC, other_arguments) or pdf(outfile) print(p_sampleQC) dev.off(). If TRUE, i) depicts the X-chromosomal heterozygosity (SNPSEX) of the samples split by their PEDSEX (if do.evaluate_check_sex is TRUE), ii) creates a scatter plot with samples' missingness rates on x-axis and their heterozygosity rates on the y-axis (if do.evaluate_check_het_and_miss is TRUE), iii) depicts all pair-wise IBD-estimates as histogram (if do.evaluate_check_relatedness is TRUE) and iv) creates a scatter plot of PC1 versus PC2 color-coded for samples of reference populations and study population (if do.check_ancestry is set to TRUE).

[logical] If TRUE, progress info is printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size of the subplot labeling.

[integer] Size for plot title.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] /path/to/directory where results will be written to. If perIndividualQC was conducted, this directory should be the same as qcdir specified in perIndividualQC, i.e. it contains name.fail.IDs with IIDs of individuals that failed QC. User needs writing permission to qcdir. Per default, qcdir=indir.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[logical] If TRUE, run check_snp_missingness.

[double] Threshold for acceptable variant missing rate across samples.

[logical] If TRUE, run check_hwe.

[double] Significance threshold for deviation from HWE.

[logical] If TRUE, run check_maf.

[double] Threshold for minor allele cut cut-off, if both mafTh and macTh are specified, macTh is used (macTh = mafTh\*2\*NrSamples).

[double] Threshold for minor allele frequency cut-off.

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_marker) via ggplot2::ggsave(p=p_marker, other_arguments) or pdf(outfile) print(p_marker) dev.off().

[logical] If TRUE, progress info is printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[integer] Size for legend text.

[integer] Size for legend title.

[integer] Size for axis text.

[integer] Size for axis title.

[integer] Size for plot title.

[integer] Size of the subplot labeling.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] If TRUE, plink log and error messages are printed to standard out.

[data.frame] containing pair-wise relatedness estimates (in column [relatednessRelatedness]) for individual 1 (in column [relatednessIID1] and individual 2 (in column [relatednessIID1]). Columns relatednessIID1, relatednessIID2 and relatednessRelatedness have to present, while additional columns such as family IDs can be present. Default column names correspond to column names in output of plink –genome (https://www.cog-genomics.org/plink/1.9/ibd). All original columns for pair-wise highIBDTh fails will be returned in fail_IBD.

[data.frame] containing a QC measure (in column [otherCriterionMeasure]) per individual (in column [otherCriterionIID]). otherCriterionMeasure and otherCriterionIID have to present, while additional columns such as family IDs can be present. IIDs in relatednessIID1 have to be present in otherCriterionIID.

[double] Threshold for filtering related individuals. Individuals, whose pair-wise relatedness estimates are greater than this threshold are considered related.

[double] Threshold for filtering individuals based on otherCriterionMeasure. If related individuals fail this threshold they will automatically be excluded.

[character] Used to determine the direction for failing the otherCriterionTh. If 'gt', individuals whose otherCriterionMeasure > otherCriterionTh will automatically be excluded. For pairs of individuals that have no other related samples in the cohort: if both otherCriterionMeasure < otherCriterionTh, the individual with the larger otherCriterionMeasure will be excluded.

[character] Column name of column containing the IDs of the first individual.

[character] Column name of column containing the IDs of the second individual.

[character, optional] Column name of column containing the family IDs of the first individual; if only relatednessFID1 but not relatednessFID2 provided, or none provided even though present in relatedness, FIDs will not be returned.

[character, optional] Column name of column containing the family IDs of the second individual; if only relatednessFID2 but not relatednessFID1 provided, or none provided even though present in relatedness, FIDs will not be returned.

[character] Column name of column containing the relatedness estimate.

[character] Column name of column containing the individual IDs.

[character] Column name of the column containing the measure of the otherCriterion (for instance SNP missingness rate).

[logical] If TRUE, progress info is printed to standard out.

[character] /path/to/directory containing the basic PLINK data files prefixMergedDataset.bim,prefixMergedDataset.fam and prefixMergedDataset.bed.

[character] Prefix of merged study and reference data files, i.e. prefixMergedDataset.bed, prefixMergedDataset.bim, prefixMergedDataset.fam.

[character] /path/to/directory to save prefixMergedDataset.eigenvec as returned by plink –pca. User needs writing permission to qcdir. Per default qcdir=indir.

[logical] If TRUE, progress info is printed to standard out.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory to save name.het as returned by plink –het. User needs writing permission to qcdir. Per default qcdir=indir.

[logical] If TRUE, progress info is printed to standard out.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory to save name.imiss as returned by plink –missing. User needs writing permission to qcdir. Per default qcdir=indir.

[logical] If TRUE, progress info is printed to standard out.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory to save name.genome as returned by plink –genome. User needs writing permission to qcdir. Per default qcdir=indir.

[double] Threshold for acceptable proportion of IBD between pair of individuals; only pairwise relationship estimates larger than this threshold will be recorded.

[double] Threshold of minor allele frequency filter for selecting variants for IBD estimation.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[logical] Should high LD regions be filtered before IBD estimation; carried out per default with high LD regions for hg19 provided as default via genomebuild. For alternative genome builds not provided or non-human data, high LD regions files can be provided via high_ldregion_file.

[character] Path to file with high LD regions used for filtering before IBD estimation if filter_high_ldregion == TRUE, otherwise ignored; for human genome data, high LD region files are provided and can simply be chosen via genomebuild. Files have to be space-delimited, no column names with the following columns: chromosome, region-start, region-end, region number. Chromosomes are specified without 'chr' prefix. For instance: 1 48000000 52000000 1 2 86000000 100500000 2

[character] Name of the genome build of the PLINK file annotations, ie mappings in the name.bim file. Will be used to remove high-LD regions based on the coordinates of the respective build. Options are hg18, hg19 and hg38. See @details.

[logical] If TRUE, plink log and error messages are printed to standard out.

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, progress info is printed to standard out.

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam.

[character] /path/to/directory to save name.sexcheck as returned by plink –check-sex. User needs writing permission to qcdir. Per default qcdir=indir.

[logical] If TRUE, progress info is printed to standard out.

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accessible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec('plink').

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

[logical] If TRUE, plink log and error messages are printed to standard out.

[list] whose elements are tested for being numeric.

[list] whose elements are tested for being positive numbers.

[list] whose elements are tested for being integers.

[list] whose elements are tested for being proportions. between 0 and 1.