bedgraph_flip: Convert bedgraph values between positive and negative

In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description

Get raw counts of reads mapped to specified genomic features using featureCount tool from the subread package.

Usage

bedgraph_flip(inFiles, outDest = "./", outSuffix = "_flipped")

Arguments

inFiles	Character - Bedgraph file list
outDest	String - Directory where output files should be saved
outSuffix	String - will be appended to original filename; default "_flipped"

Details

Take a list of bedgraph files and convert positive values to negative and vice-versa. This is a hack for getting value from two different files into the same deeptools heatmap, but with a different color scheme for each (using computeMatrix() and plotHeatmap()). Handy for being able to distinguish forward- and reverse-strand reads. TIME: 3-5 s per bedgraph, at least for ~15-20MB ones.

Author(s)

Emma Myers

Examples

bgs = list.files(pattern = "minus.bedgraph")
bedgraph_flip(bgs)

e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.