phantomPeak: QC metrics RSC and NSC

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

Description

Report the QC metrics, RSC and NSC, and plot the cross-correlation profile.

Usage

phantomPeak(chip.data, input.data, binding.characteristics,
  smoothing.bandwidth = 5)

Arguments

chip.data	spp tags of the ChIP sample calculated with calculateBindingCharacteristics.
input.data	spp tags of the input sample calculated calculateBindingCharacteristics.
binding.characteristics	The binding characteristics calculated with calculateBindingCharacteristics.
smoothing.bandwidth	Smooth the curve of the cross-correlation plot using a moving average (higher value means more smoothing).

Details

Calculate RSC and NSC metrics and plot the cross-correlation profile.

• The relative strand correlation (RSC) is the ratio between the peak of the fragment length and the peak of the read length. ENCODE guidelines recommend that the RSC be > 0.8.

• The normalized strand coefficient, NSC, is the normalized ratio between the peak of the fragment-length cross-correlation and the background cross-correlation. ENCODE guidelines recommend that the NSC be > 1.05.

Value

A vector containing the NSC, RSC, estimated read length and estimated fragment length.

Examples

# call SPP to get the binding characteristics
bc <- calculateBindingCharacteristics("IP.bam", "input.bam", read.len=51)
# plot the cross-correlation profile
pp <- phantomPeak(bc$chip.data, bc$input.data, bc$bc)

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