getPeaks: Obtain peaks from GUIDE-seq

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

Obtain peaks from GUIDE-seq

Description

Obtain strand-specific peaks from GUIDE-seq

Usage

getPeaks(
  gr,
  window.size = 20L,
  step = 20L,
  bg.window.size = 5000L,
  min.reads = 10L,
  min.SNratio = 2,
  maxP = 0.05,
  stats = c("poisson", "nbinom"),
  p.adjust.methods = c("none", "BH", "holm", "hochberg", "hommel", "bonferroni", "BY",
    "fdr")
)

Arguments

gr	GRanges with cleavage sites, output from getUniqueCleavageEvents
window.size	window size to calculate coverage
step	step size to calculate coverage
bg.window.size	window size to calculate local background
min.reads	minimum number of reads to be considered as a peak
min.SNratio	minimum signal noise ratio, which is the coverage normalized by local background
maxP	Maximum p-value to be considered as significant
stats	Statistical test, default poisson
p.adjust.methods	Adjustment method for multiple comparisons, default none

Value

peaks	GRanges with count (peak height), bg (local background), SNratio (signal noise ratio), p-value, and option adjusted p-value
summarized.count	A data frame contains the same information as peaks except that it has all the sites without filtering.

Author(s)

Lihua Julie Zhu

Examples

    if (interactive())
    {
        data(uniqueCleavageEvents)
        peaks <- getPeaks(uniqueCleavageEvents$cleavage.gr,
            min.reads = 80)
        peaks$peaks
    }

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.