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)

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

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

    prepareGeneQuantSTAR(..., 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 1.6.2 Index]