getPeaks: Obtain peaks from GUIDE-seq
In GUIDEseq: GUIDE-seq analysis pipeline

Description Usage Arguments Value Author(s) Examples

Obtain strand-specific peaks from GUIDE-seq

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"))

`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

`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.

Lihua Julie Zhu

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