cumulativePercentage: Plot the cumulative percentage of tag allocation

In jianhong/NADfinder: Call wide peaks for sequencing data

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"]])

jianhong/NADfinder documentation built on Nov. 2, 2024, 12:09 a.m.