export_ERs: Identify and Export stringent/ weak ERs

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

Description

ChIP-Seq detects genome-wide DNA protein interaction, returning enriched regions which associated with significance score. Using permissive threshold tau.s for stringent enriched region, we could identify set of stringent, weakly enriched regions by the output of runMSPC. All ERs in different group can be exported as either BED format file by using export.bed, or csv by write.csv.

Usage

export_ERs(peakList_A, peakList_B, tau.s = 1e-08, exportFormat = c("bed",
  "csv"))

Arguments

peakList_A	output of runMSPC, is set of ERs that fulfill combined stringency test, rescued by Fisher's method, also known as confirmed ERs.
peakList_B	output of runMSPC, is set of discarded ERs that failing from combined stringency test and minimum overlapping peak requirement
tau.s	permissive threshold value for stringent ERs, all ERs' pvalue below this value, are considered as stringent ERs.
exportFormat	user has an option to export the result either BED format file or csv.

Value

stringent/weak peak set

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)
discardedERs <- runMSPC(peakset = total.ERs, whichType = "max",
                        cmbStrgThreshold = 1.0E-08, isConfirmed = FALSE)

## explore the peaks in different output set for file bar
export_ERs(peakList_A = confirmedERs,
           peakList_B = discardedERs,
           tau.s = 1.0E-08, exportFormat = "csv")

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