cumulativePercentage {ChIPpeakAnno} | R Documentation

## 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)

[Package ChIPpeakAnno version 3.26.4 Index]