trimPeaks {NADfinder} | R Documentation |
Filter the peaks by pvalue and trim the range of peaks for an NAD experiment without biological replicates.
trimPeaks(se, cutoffPvalue = 0.05, backgroundPercentage = 0.25, countFilter = 1000, ratioAssay = "ratio", backgroundCorrectedAssay = "bcRatio", smoothedRatioAssay = "smoothedRatio", zscoreAssay = "zscore")
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. |
An object of GRanges.
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)