tagCount: ChIP-seq binned tag counting tool

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

Description

tagCount returns a data.frame of tag counts per bin per sample.

Usage

tagCount(samples, org, assembly, version, binSize = 1000, cluster = NULL)

Arguments

samples	List/vector of paths or list of GAlignments/BamFile/BamViews objects or GAlignmentsList or BamFileList that will be processed.
org	The organism as described in the BSGenome package: Hsapiens, Mmusculus, ...
assembly	The assembly name: UCSC, NCBI, TAIR, ...
version	The assembly version: hg19, mm9, ...
binSize	The size of the bins.
cluster	A snow cluster to process samples in parallel: cluster <- snow::makeCluster(cores).

Details

This function makes use of the GenomicAlignments package to count tags on bins. The reference genome is split into bins and a data.frame with the counts per bin is returned. The data.frame has one column for each sample.

Value

A data.frame with counts on bins. Each column contains the counts of one sample.

Examples

counts <- tagCount(
    samples=c("ctl1.bam", "ctl2.bam", "chip1.bam", "chip2.bam"),
    org="Mmusculus", assembly="UCSC", version="mm9"
)
nCounts <- normalizeTagCount(counts)
topHeatmap(nCounts)
samplesHeatmap(nCounts)
pcaPlot(nCounts, as.factor(c("ctl", "ctl", "chip", "chip")))

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