parseVarScan: Parse a VarScan output

In rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis

Description

Separate the pool and sample call information into usable columns.

Usage

parseVarScan(file, sampleNames = NULL, ignoreIndels = TRUE)

Arguments

file	Either a character vector of length 1 giving the name of a tab-separated VarScan file to read in, or a data.frame or matrix containing the VarScan output table.
sampleNames	A character vector giving the names to assign to the split sample calls.
ignoreIndels	Logical: should positions with indels be omitted from the returned file (default: TRUE)

Details

This assumes that the headers have not been modified

Value

Returns a data.frame with rows for each row (ommiting the indels if ignoreIndels == TRUE), but with each portion of the calls separated.

Author(s)

Mark Peterson

References

Relies on the VarScan output documented here: http://varscan.sourceforge.net/using-varscan.html

Examples

## Get example data
## This could be just read in using read.table for your data
data(varScanExample)

parseTest <- parseVarScan(varScanExample,
                          sampleNames=LETTERS[1:10])

head(parseTest)

rnaseqWrapper documentation built on May 2, 2019, 5:58 a.m.