diff_peaks: Identify differential peaks

In jiang-junyao/IReNA: IReNA

Identify differential peaks

Description

Identify differential peaks based on edgeR, samples of peaks need to be divided into at least two groups.

Usage

diff_peaks(Count, Group)

Arguments

Count	data.frame, indicating counts of peaks, generated by htseq-count. If you calculate counts for each sample separately, you need to run merge_sort_count() function firstly.
Group	vector or factor giving the experimental group/condition for each sample/library.

Value

return FDR q-value and foldchange of each peak, which can be used to identify differential peaks.

Examples

load(system.file("extdata", "test_peak.rda", package = "IReNA"))
group <- c(1,1,2,2)
peaks <- diff_peaks(test_peak[,4:7],group)

jiang-junyao/IReNA documentation built on Nov. 4, 2024, 8:29 p.m.