cumulativePercentage {NADfinder} | R Documentation

## Plot the cumulative percentage of tag allocation

### Description

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

### Usage

    cumulativePercentage(
      se,
      binWidth = 1e+05,
      backgroundCorrectedAssay = "bcRatio",
      ...
    )

### Arguments

`se` | An object of RangedSummarizedExperiment with assays of raw counts, transfomred ratios, background correct ratios, smoothed ratios and z-scores. It should be an element of the output of smoothRatiosByChromosome.
`binWidth` | numeric(1) or integer(1). The width of each bin.
`backgroundCorrectedAssay` | character(1). Assays names for background correction ratios.
`...` | Parameter not used.

### Value

A list of data.frame with the cumulative percentages.

### 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

    library(SummarizedExperiment)
    data(triplicate.count)
    se <- triplicate.count
    se <- log2se(se, transformation = "log2CPMRatio",
                 nucleolusCols = c("N18.subsampled.srt-2.bam",
                 "N18.subsampled.srt-3.bam",
                 "N18.subsampled.srt.bam"),
                 genomeCols = c("G18.subsampled.srt-2.bam",
                 "G18.subsampled.srt-3.bam",
                 "G18.subsampled.srt.bam"))
    se <- smoothRatiosByChromosome(se, chr="chr18")
    cumulativePercentage(se[["chr18"]])

[Package NADfinder version 1.12.0 Index]