IPstrength: Plot IP strength

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

Description

Plot IP strength in the way described in the CHANCE paper.

Usage

IPstrength(IP, input)

Arguments

IP	tag counts of ChIP sample as produced by tagCount.
input	tag counts of input sample as produced by tagCount.

Details

Plot IP strength in the way described in the CHANCE paper:

Ref: Diaz, A et al. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012 March 31

The process follows these steps:

1. Tile the genome into bins and count the tags on each bin.

2. Sort bins of IP sample and sort input in the same order.

3. Calculate for IP and input the cumulative sum of reads.

4. Calculate for IP and input the cumulative percentages.

5. Calculate the alpha scaling factor (ratio of cumulative sums between IP and input at the bin with the highest difference).

6. Plot IP strength.

Value

The two metrics, alpha and enrichment.

Examples

counts <- tagCount(
    samples=c("IP.bam", "input.bam"),
    org="Hsapiens", assembly="UCSC", version="hg19"
)
IPstrength(counts["IP.bam"], counts["input.bam"])

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