Prepare user-provided files to be loaded into psichomics

Usage

prepareSRAmetadata(file, output = "psichomics_metadata.txt")

prepareJunctionQuant(
  ...,
  output = "psichomics_junctions.txt",
  startOffset = NULL,
  endOffset = NULL
)

prepareGeneQuant(
  ...,
  output = "psichomics_gene_counts.txt",
  strandedness = c("unstranded", "stranded", "stranded (reverse)")
)

Arguments

file: Character: path to file
output: Character: path of output file (if NULL, only returns the data without saving it to a file)
...: Character: path of (optionally named) input files (see Examples)
startOffset: Numeric: value to offset start position
endOffset: Numeric: value to offset end position
strandedness: Character: strandedness of RNA-seq protocol; may be one of the following: unstraded, stranded or stranded (reverse)

Value

Prepared file (if output != NULL) and object

Examples

if (FALSE) { # \dontrun{
prepareJunctionQuant("Control rep1"=junctionFile1,
                     "Control rep2"=junctionFile2,
                     "KD rep1"=junctionFile3,
                     "KD rep2"=junctionFile4)
} # }
if (FALSE) { # \dontrun{
prepareGeneQuant("Control rep1"=geneCountFile1,
                 "Control rep2"=geneCountFile2,
                 "KD rep1"=geneCountFile3,
                 "KD rep2"=geneCountFile4)
} # }