getPeaks {GUIDEseq} | R Documentation |
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 }