callPeaks: Call peaks using SPP

In imbforge/encodeChIPqc: A set of useful ChIPseq QC metrics from the ENCODE project

Description

Call peaks using the spp package.

Usage

callPeaks(chip.data, input.data, binding.characteristics, fdr = 0.01,
  method = tag.wtd, window.size = 1000, z.thr = 3, cluster = NULL)

Arguments

chip.data	spp tags of the ChIP sample calculated with calculateBindingCharacteristics.
input.data	spp tags of the input sample calculated with calculateBindingCharacteristics.
binding.characteristics	The binding characteristics calculated with calculateBindingCharacteristics.
fdr	Peaks with a corrected p-value above this threshold are not reported.
method	The peak calling method, either tag.wtd or tag.lwcc.
window.size	The window size to be used in calculating enrichment.
z.thr	A z-score corresponding to the Poisson ratio threshold used to flag significantly enriched windows.
cluster	A snow cluster: cluster <- snow::makeCluster(cores).

Details

callPeaks() uses the spp package to identify regions enriched with reads (peaks) when comparing a ChIP sample to a control sample.

Value

spp peak data as generated by find.binding.positions and add.broad.peak.regions.

Examples

bc <- calculateBindingCharacteristics("IP.bam", "input.bam", read.len=51)
peaks <- callPeaks(bc$chip.data, bc$input.data, bc$bc)

imbforge/encodeChIPqc documentation built on May 18, 2019, 4:45 a.m.