calculateBindingCharacteristics: Get binding characteristics

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

Description

Get binding characteristics from cross-correlation profile using the spp package.

Usage

calculateBindingCharacteristics(IP, input, read.len = NULL,
  min.shift = -500, max.shift = 1500, bin.size = 5, cluster = NULL)

Arguments

IP	File name/GAlignments object/spp tags of IP sample.
input	File name/GAlignments object/spp tags of input sample.
read.len	Read length. If NULL, the read length is detected automatically by using the median of the first 10,000 reads in the first ChIP sample.
min.shift	Minimum shift range.
max.shift	Maximum shift range.
bin.size	Bin tags within the specified number of basepairs to speed up calculation.
cluster	A snow cluster: cluster <- snow::makeCluster(cores).

Details

Types of analysis:

• Calculate binding characteristics.

• Report QC metrics, RSC and NSC.

• Calculate genome-wide profiles of smoothed tag density.

• Calculate genome-wide profiles providing conservative statistical estimates of fold enrichment.

• Determine statistically significant point binding positions.

• Assessing saturation properties.

Value

A list with the ChIP data, the input data and the binding characteristics.

Examples

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

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