trimPeaks: Trim peaks

In jianhong/NADfinder: Call wide peaks for sequencing data

Trim peaks

Description

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

Usage

trimPeaks(
  se,
  cutoffAdjPvalue = 0.05,
  padjust.method = "BH",
  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
cutoffAdjPvalue	numeric(1). Cutoff of adjusted p-value.
padjust.method	character(1). The method to use for adjusting p-values, which is passed to p.adjust function
backgroundPercentage	numeric(1). Cutoff value for the peaks height.
countFilter	numeric(1) or integer(1). Cutoff value for mean of raw reads count of the Nucleolar/ChIP samples 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,
                cutoffAdjPvalue=0.05, countFilter=1000)

jianhong/NADfinder documentation built on Oct. 29, 2023, 11:08 a.m.