getPeaks: Obtain peaks from GUIDE-seq

Description Usage Arguments Value Author(s) Examples

View source: R/getPeaks.R

Description

Obtain strand-specific peaks from GUIDE-seq

Usage

1
2
3
4
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

1
2
3
4
5
6
7
    if (interactive())
    {
        data(uniqueCleavageEvents)
        peaks <- getPeaks(uniqueCleavageEvents$cleavage.gr,
            min.reads = 80)
        peaks$peaks
    }

GUIDEseq documentation built on May 31, 2017, 3:06 p.m.

Search within the GUIDEseq package
Search all R packages, documentation and source code