getPeaks {GUIDEseq} | R Documentation

## 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
        }

[Package GUIDEseq version 1.20.0 Index]