Single Nucleotide Polymorphisms Linkage Disequilibrium
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Documentation for package ‘snplinkage’ version 1.2.0
Help Pages
| %$% | Exposition pipe |
| %<>% | Assignment pipe |
| %>% | Pipe |
| chisq_pvalues | Compute Chi-squared p-values |
| chisq_pvalues_gdata | Compute Chi-squared p-values on a Genotype data object |
| crohn | Crohn's disease data |
| diamond_annots | Get diamond ggplot layer. |
| fetch_allele1.default | Fetch allele 1 (default object) |
| fetch_allele1.GdsGenotypeReader | Fetch allele 1 (GdsGenotypeReader object) |
| fetch_allele1.GenotypeData | Fetch allele 1 (GenotypeData object) |
| fetch_allele1.GenotypeDataSubset | Fetch allele 1 (GenotypeDataSubset object) |
| fetch_allele2.default | Fetch allele 2 (default object) |
| fetch_allele2.GdsGenotypeReader | Fetch allele 2 (GdsGenotypeReader object) |
| fetch_allele2.GenotypeData | Fetch allele 2 (GenotypeData object) |
| fetch_allele2.GenotypeDataSubset | Fetch allele 1 (GenotypeDataSubset object) |
| fetch_gds.default | Fetch GDS (default) |
| fetch_gds.GdsGenotypeReader | Fetch GDS (GdsGenotypeReader) |
| fetch_gds.GenotypeData | Fetch GDS (GenotypeData) |
| fetch_gds.GenotypeDataSubset | Fetch GDS (GenotypeDataSubset) |
| gdata_add_gene_annots | gdata_add_gene_annots |
| gdata_add_gene_annots_aim_example | gdata_add_gene_annots_aim_example |
| gdata_add_gene_annots_hladr_example | gdata_add_gene_annots_hladr_example |
| gdata_scans_annots | gdata_scan_annots |
| gdata_snps_annots | gdata_snp_annots |
| get_biomart_metadb | get_biomart_metadb |
| get_scan_annot.GenotypeData | Get scans annotations (GenotypeData object) |
| get_scan_annot.GenotypeDataSubset | Get scans annotations (GenotypeDataSubset object) |
| get_snp_annot.GenotypeData | Get SNPs annotations (GenotypeData object) |
| get_snp_annot.GenotypeDataSubset | Get SNPs annotations (GenotypeDataSubset object) |
| ggplot_associations | Ggplot associations |
| ggplot_ld | Ggplot linkage disequilibrium |
| ggplot_snp_pos | Ggplot SNPs position |
| gtable_ld | Gtable of linkage disequilibrium and chromosomic positions |
| gtable_ld_associations | Gtable of linkage disequilibrium and associations |
| gtable_ld_associations_combine | Build gtable by combining ggplots |
| gtable_ld_associations_gdata | Gtable of linkage disequilibrium and associations using a GenotypeData object |
| gtable_ld_gdata | Gtable of linkage disequilibrium and positions using a GenotypeData object |
| gtable_ld_grobs | Build gtable by combining ggplots |
| is_snp_first_dim.default | Is SNP first dimension (default) |
| is_snp_first_dim.gds.class | Is SNP first dimension (GDS object) |
| is_snp_first_dim.GdsGenotypeReader | Is SNP first dimension (GdsGenotypeReader object) |
| is_snp_first_dim.GenotypeData | Is SNP first dimension (GenotypeData object) |
| is_snp_first_dim.MatrixGenotypeReader | Is SNP first dimension (MatrixGenotypeReader object) |
| is_snp_first_dim.NcdfGenotypeReader | Is SNP first dimension (NcdfGenotypeReader object) |
| load_gds_as_genotype_data | Load GDS as Genotype Data |
| parallel_apply | Separate a matrix in a list of matrices of length the number of cores and apply a function on the columns in parallel |
| print_qc_as_tex_table | print_qc_as_tex_table |
| save_hgdp_as_gds | save_hgdp_as_gds |
| select_region_idxs | select_region_idxs |
| snprelate_allele_frequencies | Compute allele frequencie and snp missing rate |
| snprelate_ld | Wrapper for snpgdsLDMat to compute r2 |
| snprelate_ld_select | Wrapper for snpgdsLDpruning to select Tag SNPs |
| snprelate_qc | snprelate_qc |