consensusPeaks: Get consensus peaks

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Get consensus peaks

Description

Get the consensus peaks for ChIP-seq or ATAC-seq peaks.

Usage

  consensusPeaks(x)

Arguments

x	GRangesList(1): a list of peaks in GRanges. The first GRanges has to contain the peaks from pooled reads. The other GRanges are assumed to be peaks called from each replicate.

Details

To deal with the replicates and get the consensus peaks, the strategy is to pool the reads from replicates and call the peaks.

This function produces a much more conservative set of peaks. For each peak from pooled reads, the peak is kept only when the overlap with the peak from each replicate is larger than half of either peak.

Value

GRanges object of final peaks.

Author(s)

Ge Tan

Examples

  ## Not run: 
    ## consensusPeaks
    bedFns <- file.path("/srv/gstore/projects/p2578/MACS2_22192_2018-01-29--14-07-06",
                        c("A0062P_peaks.bed", "A0101P_peaks.bed", 
                          "A3401P_peaks.bed"))
    bedGRL <- GRangesList(lapply(bedFns, import.Macs2Peaks))
    consensusPeaks(bedGRL)
  
## End(Not run)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.