alignFeature: Read counts relative to annotated features

In ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

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.

Author(s)

Peter Humburg

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)

ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.