FDR_stats: Multiple testing correction

In julaiti/MSPC: Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks

Description

Given the output of runMSPC, we obtained set of peak which comply with combined stringency test by Fisher method, and classified as confirmed peaks. However, we need to further evaluate set of confirmed peaks with multiple testing corrections procedure, and produce final output set.

Usage

FDR_stats(peakList, pAdjustMethod = "BH", fdr = 0.05, asPlot = TRUE)

Arguments

peakList	set of confirmed peaks through combined stringency test.
pAdjustMethod	pvalue adjustment method
fdr	parameter for false discovery rate
asPlot	logical whether produce graphical plot or not

Value

set of enriched regions in BED format file

Author(s)

Jurat Shahidin

Examples

# set up
library(GenomicRanges)
library(rtracklayer)

# load peak files
files <- getPeakFile()[1:3]
grs <- readPeakFiles(files, pvalueBase=1L)

## Exclude background noise
total.ERs <- denoise_ERs(peakGRs = grs, tau.w = 1.0E-04,
                        overwrite = TRUE)

## explore set of confirmed, discarde peaks
confirmedERs <- runMSPC(peakset = total.ERs, whichType = "max",
                        cmbStrgThreshold = 1.0E-08, isConfirmed = TRUE)

# multiple testing correction
FDR_stats(peakList = confirmedERs,
          pAdjustMethod = "BH",
          fdr = 0.05, asPlot =FALSE )

julaiti/MSPC documentation built on Oct. 17, 2019, 9:44 p.m.