readPeakFiles: Import Chip-seq replicates and all ERs are stored in GRanges...

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

Description

This function can read peak file in standard BED file using import.bed or data.frame like object using makeGRangesFromDataFrame and stored in GRanges object, where several peak files can be read simultaneously using lapply. Note that some data sources provide ChIP-Seq enriched regions without p-value under specific conditions. In our workflow, we are going to evaluate each peak interval with p-value threshold, so represent peak's score as p-value is needed.

Usage

readPeakFiles(peakFolder, pvalueBase = 1L, verbose = FALSE)

Arguments

peakFolder	ChipSeq peak replicate either in BED format or data.frame
pvalueBase	User has option to select p-value format (- log(p.value), -10 log(p.value), -100 log(p.value))
verbose	logical that control whether the output is printed or not

Details

Passed to denoise_ERs

Value

GRanges object

Author(s)

Jurat Shahidin

Examples

require(rtracklayer)
require(GenomicRanges)

## get bed file
files <- getPeakFile()[1:3]
readPeakFiles(files, pvalueBase=1L)

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