countReads: Count Reads

In jmc200/Rcade: R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data

Description

Most Rcade users will not need to call this function directly. Given targets information linking to bam files, count the reads that lie in defined bins.

Usage

countReads(annoZone, targets, fileDir=NULL, dontCheckTargets=FALSE)

Arguments

annoZone	GRanges - The bins to be used when counting reads.
targets	data.frame - Targets file (see vignette)
fileDir	character - The directory in which the raw ChIP-seq data files are kept.
dontCheckTargets	logical - If TRUE, the targets file is not checked for consistency/appropriate field names. This should not be changed for Rcade purposes, but may be useful if you wish to obtain bin counts for some other purpose. Make sure relevant column names are lower case. Use at your own risk!

Value

Matrix of read counts, with columns corresponding to samples and rows corresponding to bins.

Author(s)

Jonathan Cairns

See Also

RcadeAnalysis

Examples

	dir <- file.path(system.file("extdata", package="Rcade"), "STAT1")

	targets <- read.csv(file.path(dir, "targets.csv"), as.is = TRUE)

	anno <- read.csv(file.path(dir, "anno.csv"))
	anno <- anno[order(anno$chromosome_name),]
	colnames(anno) <- c("ENSG","chr","start","end","str")
	ChIPannoZones <- defineBins(anno, zone=c(-1500, 1500), geneID="ENSG")

	x <- countReads(ChIPannoZones, targets, fileDir = dir)

jmc200/Rcade documentation built on June 17, 2020, 5:59 a.m.