prepareSRAmetadata: Prepare user-provided files to be loaded into psichomics

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Description

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

## Not run: 
prepareJunctionQuant("Control rep1"=junctionFile1,
                     "Control rep2"=junctionFile2,
                     "KD rep1"=junctionFile3,
                     "KD rep2"=junctionFile4)

## End(Not run)
## Not run: 
prepareGeneQuant("Control rep1"=geneCountFile1,
                 "Control rep2"=geneCountFile2,
                 "KD rep1"=geneCountFile3,
                 "KD rep2"=geneCountFile4)

## End(Not run)

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.