prepareSRAmetadata {psichomics}R Documentation

Prepare files to be loaded into psichomics

Description

Prepare 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 to file(s) to read

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

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)
[Package psichomics version 1.8.2 Index]