callPeak: Call peaks

In jianhong/diffPeaks: Quantifying Differential Features

Description

Calling peaks from bam files

Usage

callPeak(bamfile, index = bamfile, inputBam = NULL,
  inputIndex = inputBam, txdb, genome, upstream = 50000,
  downstream = 50000, ideaPeakWidth = 200, FDRfilter = 0.05,
  direction = c("over", "less"))

Arguments

bamfile	bam file name
index	index file name
inputBam	input bam file name
inputIndex	index file name for input
txdb	TxDb object
genome	BSgenome object
upstream	peak scan start position from upstream of gene
downstream	peak scan end position till downstream of gene
ideaPeakWidth	ideally peak width, eg, ATAC-seq: 200bp
FDRfilter	cut off value of FDR.
direction	over or less. In most case, default over is OK. In some cases, such as cohesion, less may be what you want to try.

Value

a GRanage object indicates the peaks.

Examples

path <- system.file("extdata", package = "diffPeaks", mustWork = TRUE)
bamfiles <- dir(path, "bam$", full.names = TRUE)
bamfile <- bamfiles[1]
index <- bamfile
library(TxDb.Drerio.UCSC.danRer10.refGene)
txdb <- TxDb.Drerio.UCSC.danRer10.refGene
library(BSgenome.Drerio.UCSC.danRer10)
genome <- Drerio
upstream <- downstream <- 50000L
ideaPeakWidth <- 200
direction <- "over"
x <- callPeak(bamfile, txdb=txdb, genome=genome)

jianhong/diffPeaks documentation built on May 22, 2019, 12:37 p.m.