fix.macs.output: fix MACS result files

In drmjc/macsR: Facilitate analysis of MACS results.

Description

MACS (Model-based Analysis of ChIP-Seq) is a very popular program for identifying peaks in ChIP-Seq data. It's output is pretty good, but IMO can be improved:
- The peaks XLS files could be a proper XLS files - the -10*LOG10(pvalue) in peaks xls files is confusing, so create a proper P-value column - There is no “name” column in the peaks xls files to match up to the names in the BED files - an IGV/UCSC-friendly coordinate aids following up regions - useful to have BED files at various FDR thresholds. It's also useful to make BED files with only the statistically significant peaks within.

Usage

  fix.macs.output(dir, fdr.thresh = c(5, 10, 15, 25))

Arguments

dir	a character(1) pointing to a directory containing MACS results
fdr.thresh	an integer vector: Create 1 BED file per fdr.thresh, containing only those peaks with FDR < fdr.thresh, named ...-fdr%d.xls. Note in these files FDR are represented as percentages, so we suggest starting with c(5, 10, 25), Set to NULL to skip this step.

Value

Invisibly returns the positive peaks table. It destructively edits some files in a MACS results directory, but does save the original peaks.xls files as *peaks_original.xls

Author(s)

Mark Cowley, 2012-01-30

Examples

## Not run: 
fix.macs.output("/path/to/macs/results")
fix.macs.output("/path/to/macs/results", fdr.thresh=10)
fix.macs.output("/path/to/macs/results", fdr.thresh=c(5,10,25))
peaks <- fix.macs.output("/path/to/macs/results")

## End(Not run)

drmjc/macsR documentation built on May 15, 2019, 2:23 p.m.