cumulativePercentage: Plot the cumulative percentage tag allocation in sample

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Plot the difference between the cumulative percentage tag allocation in paired samples.

Usage

cumulativePercentage(bamfiles, gr, input = 1, binWidth = 1000, ...)

Arguments

bamfiles	Bam file names.
gr	An object of GRanges
input	Which file name is input. default 1.
binWidth	The width of each bin.
...	parameter for summarizeOverlaps.

Value

A list of data.frame with the cumulative percentages.

Author(s)

Jianhong Ou

References

Normalization, bias correction, and peak calling for ChIP-seq Aaron Diaz, Kiyoub Park, Daniel A. Lim, Jun S. Song Stat Appl Genet Mol Biol. Author manuscript; available in PMC 2012 May 3.Published in final edited form as: Stat Appl Genet Mol Biol. 2012 Mar 31; 11(3): 10.1515/1544-6115.1750 /j/sagmb.2012.11.issue-3/1544-6115.1750/1544-6115.1750.xml. Published online 2012 Mar 31. doi: 10.1515/1544-6115.1750 PMCID: PMC3342857

Examples

## Not run: 
path <- system.file("extdata", "reads", package="MMDiffBamSubset")
files <- dir(path, "bam$", full.names = TRUE)
library(BSgenome.Hsapiens.UCSC.hg19)
gr <- as(seqinfo(Hsapiens)["chr1"], "GRanges")
cumulativePercentage(files, gr)

## End(Not run) 
 

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.