Input/Output Utilities of the 'ribios' Suite

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Documentation for package ‘ribiosIO’ version 1.1.0

• DESCRIPTION file
• Package NEWS
• Package README

Help Pages

as.matrix.GctMatrix	Coerce a GctMatrix object into a matrix
as_numeric_matrix	Transform a data.frame to a numeric matrix without characters coereced as factors
cbindGct	Column bind (cbind) two GctMatrix objects
find_ampliseq	Find and read-in AmpliSeq files
find_and_read_ampliseq	Find and read-in AmpliSeq files
gctDesc	Retrieve feature (row) descriptions from a GctMatrix S3-object
GctMatrix	Create a GctMatrix object
gctMatrix2longdf	Convert a GctMatrix into a long data frame
getDataDir	Get the data directory
iofile	Get file names for data import/export
isGctFile	Test a file is a GCT file or not
is_cls_file	Check if a file encodes a factor
is_factor_file	Check if a file encodes a factor
loadFile	Attempt to load a binary RData file
loadObject	Load an object by its name from a RData file
loadObjectInEnv	Load objects from a RData file and return them in an environment
loadRDS	Load an object from a RDS file and returns a logical flag
longdf2gctMatrix	Convert a long data.frame into a GctMatrix
optional_suppress_warning	Supress warning optionally
print.GctMatrix	Print method for GctMatrix object
readMatrix	Read in numeric matrix from tab-delimited format written by 'writeMatrix'
readTable	Read in data.frame from tab-delimited format written by 'writeMatrix'
read_ampliseq	Find and read-in AmpliSeq files
read_ampliseq_bedcovgct	Read bedcov output of AmpliSeq amplicons and convert them to read counts
read_annotated_ampliseq_amplicons	Read AmpliSeq amplicon informaiton from an annotated BED file
read_bed	Read a BED file
read_biokit_exprs	qRead BioKit expression file into a data.frame
read_chip	Read CHIP file
read_cls	Read in a factor writtin in the CLS format
read_david	Read tab-delimited result files from DAVID Bioinformatics Resources
read_exprs_matrix	Read an expression matrix from file
read_factor	Read in a factor writtin in the CLS format
read_fasta	Read (write) FASTA sequences into (from) named character vectors
read_gct	Calling C routine to read GCT file into a matrix
read_gctstr_matrix	Calling C routine to read GCT file into a matrix
read_gct_matrix	Calling C routine to read GCT file into a matrix
read_gmt	Calling C routine to read GMT file into a list
read_gmt_dataframe	Read gene-sets in a GMT file into a data.frame
read_gmt_list	Calling C routine to read GMT file into a list
read_illumina_sampleSheet	Read the Data block of Illumina sample sheet as data.frame
read_pheno	Read pheno data from CLS or tab-delimited file
read_pheno_factor	Read pheno data from CLS or tab-delimited file
read_raw_ampliseq_amplicons	Read AmpliSeq amplicon informaiton from an raw BED file
read_trimmed_lines	Read lines, thereby trimming empty spaces around the strings and removing empty lines
setDataDir	Set the data directory
strList2DataFrame	Format a string list into a data.frame
write.tableList	Write a list of data.frames (tables) into files
writeMatrix	Export matrix into a commonly used tab-delimited format inside Roche Bioinformatics
writeMatrix.tableList	Write a list of data.frames (tables) into file with writeMatrix
writeStrList	Write a list of strings in a tab-delimited file
write_annotated_ampliseq_amplicons	Write AmpliSeq amplicon informaiton into an annotated BED file
write_cls	Write a factor in the CLS format
write_factor	Write a factor in the CLS format
write_fasta	Read (write) FASTA sequences into (from) named character vectors
write_gct	Write matrix in GCT file format
write_gmt	Write a list of gene sets into a GMT file
[.GctMatrix	Subsetting for GctMatrix