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

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Prepare user-provided files to be loaded into psichomics

Description

Prepare user-provided files to be loaded into psichomics

Usage

prepareJunctionQuantSTAR(..., startOffset = -1, endOffset = +1)

prepareGeneQuantSTAR(
  ...,
  strandedness = c("unstranded", "stranded", "stranded (reverse)")
)

Arguments

...	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)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.