R: Input/Output Utilities of the 'ribios' Suite

# Input/Output Utilities of the 'ribios' Suite

## 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