trimPeaks | R Documentation |
Filter the peaks by pvalue and trim the range of peaks for an NAD or ChIP-seq experiment without biological replicates.
trimPeaks(
se,
cutoffAdjPvalue = 0.05,
padjust.method = "BH",
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 |
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. |
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,
cutoffAdjPvalue=0.05, countFilter=1000)
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