normalizeTagCount: Normalize tag counts

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

Description

Normalize tag counts produced by tagCount by total tag count.

Usage

normalizeTagCount(counts, n = 500)

Arguments

counts	The output of tagCount.
n	Limit the output to the top n bins with the greatest variance. The default value of 500 is usually sufficient for clustering. NULL means all bins are returned.

Details

This function normalizes the tag counts produced by tagCount. The tag counts per bin are scaled, such that each sample has as many normalized tags as the sample with the most tags.

Value

A data.frame with normalized 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.