trimPeaks {NADfinder} | R Documentation

## 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)

[Package NADfinder version 1.14.0 Index]