trimPeaks: Trim peaks

In LihuaJulieZhu/NADfinder: Call wide peaks for sequencing data

Description

Filter the peaks by pvalue and trim the range of peaks for an NAD experiment without biological replicates.

Usage

trimPeaks(se, cutoffPvalue = 0.05, backgroundPercentage = 0.25,
  countFilter = 1000, ratioAssay = "ratio",
  backgroundCorrectedAssay = "bcRatio",
  smoothedRatioAssay = "smoothedRatio", zscoreAssay = "zscore")

Arguments

se	An object of RangedSummarizedExperiment with assays of raw counts, ratios, background corrected ratios, smoothed ratios and z-scores. It should be an element of the output of smoothRatiosByChromosome
cutoffPvalue	numeric(1). Cutoff p-value.
backgroundPercentage	numeric(1). Cutoff value for the peaks height.
countFilter	numeric(1) or integer(1). Cutoff value for mean of raw reads count in each window.
ratioAssay	character(1). The name of assay in se, which store the values to be smoothed.
backgroundCorrectedAssay, smoothedRatioAssay, zscoreAssay	Assays names for background-corrected ratios, smoothed ratios and z-scores based on background corrected ratios.

Value

An object of GRanges.

Examples

data(single.count)
se <- single.count
dat <- log2se(se, nucleolusCols="N18.subsampled.srt.bam", genomeCols="G18.subsampled.srt.bam", 
transformation="log2CPMRatio")
## Smooth the ratios for each chromosome.
dat <- smoothRatiosByChromosome(dat, N=100, chr=c("chr18","chr19"))
peaks <- trimPeaks(dat[["chr18"]],
                backgroundPercentage=.25,
                cutoffPvalue=0.05, countFilter=1000)

LihuaJulieZhu/NADfinder documentation built on May 17, 2019, 6:21 p.m.