GctMatrix               Create a GctMatrix object
[.GctMatrix             Subsetting for GctMatrix
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
gctDesc                 Retrieve feature (row) descriptions from a
                        GctMatrix S3-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_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_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_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_matrix         Calling C routine to read GCT file into a
                        matrix
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_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_factor            Write a factor in the CLS format
write_gct               Write matrix in GCT file format
write_gmt               Write a list of gene sets into a GMT file
