cumulativePercentage {NADfinder} | R Documentation |
Plot the difference between the cumulative percentage of tag allocation in paired samples.
cumulativePercentage(se, binWidth = 1e+05, backgroundCorrectedAssay = "bcRatio", ...)
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. |
A list of data.frame with the cumulative percentages.
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
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"]])