cumulativePercentage: Plot the cumulative percentage tag allocation in sample

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Plot the cumulative percentage tag allocation in sample

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) 
 

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.