trimPeaks {NADfinder} | R Documentation

## Trim peaks

### 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)

[Package NADfinder version 1.4.0 Index]