denoise_ERs: Data cleaning

In julaiti/MSPC: Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks

Description

Given the output of readPeakFiles, We set up permissive p-value threshold tau.w for weakly enriched regions associated with score and p-value. We are interested in moderately enriched regions , but extremely weakly enriched regions must be removed from all candidate sample because it will not give any biological insight. Note that p-value threshold can be tuned by users, so using different threshold value will result in different filtering results. Background signal (A.K.A, noise) also exported as standard BED file by using export.bed for the sake of evaluate each ChIP-Seq replicate that bearing different output set with clear biological evidence.

Usage

denoise_ERs(peakGRs, tau.w = 1e-04, nmtab = "noise", dest.dir = tempdir(),
  overwrite = FALSE)

Arguments

peakGRs	Chip-seq replicate imported and all enriched regions stored in GRanges objects
tau.w	permissive p-value threshold for weakly enriched peak, all enrichred regions' pvalue above this thrshold, are considered background noise
nmtab	Character string that assigned as name to the noise
dest.dir	dirctory that exported files can be placed. only noise can be exported as standard BED file;
overwrite	default FALSE indicating whether existing files with identical name should be over-written.

Details

Passed to runMSPC

Value

Peaks without background noise is stoted in GRangesList

Author(s)

Jurat Shahidin

Examples

require(rtracklayer)
require(GenomicRanges)

## read peak file as GRanges object
files <- getPeakFile()[1:3]
grs <- readPeakFiles(files, pvalueBase=1L)

## Exclude background noise
total.ERs <- denoise_ERs(peakGRs = grs, tau.w = 1.0E-04,
                        nmtab = "noise", dest.dir = getwd(), overwrite = TRUE)
## Explore all stringent and weak enriched regions
total.ERs

julaiti/MSPC documentation built on Oct. 17, 2019, 9:44 p.m.