ChIPseqR (version 1.26.0)

alignFeature: Read counts relative to annotated features

Description

Creates a set of (strand specific) read counts centred at the genomic features provided.

Usage

alignFeature(data, anno, offset = 1000)

Arguments

data

List with read counts as returned by strandPileup.

anno

Data frame with annotation data in GFF format.

offset

Half width of window around start point of annotated features.

Value

List with one component for each feature in anno.

References

The GFF file format specification: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

Examples

set.seed(1)

## determine binding site locations
b <- sample(1:8.5e5, 500)

## sample read locations
fwd <- unlist(lapply(b, function(x) sample((x-83):(x-73), 20, replace=TRUE)))
rev <- unlist(lapply(b, function(x) sample((x+73):(x+83), 20, replace=TRUE)))

## add some background noise
fwd <- c(fwd, sample(1:(1e6-25), 5000))
rev <- c(rev, sample(25:1e6, 5000))

## create data.frame with read positions as input to strandPileup
reads <- data.frame(chromosome="chr1", position=c(fwd, rev), 
	length=25, strand=factor(rep(c("+", "-"), times=c(15000, 15000))))

## create object of class ReadCounts
readPile <- strandPileup(reads, chrLen=1e6, extend=1, plot=FALSE)

## convert binding site locations into GFF format
gff <- data.frame(chromosome="chr1", source="test", feature="binding", start=b-73, end=b+73, 
	score=".", strand=".", frame=".")

## align read counts relative to binding site location
aligned <- alignFeature(readPile, gff, offset=500)