alignFeature {ChIPseqR} | R Documentation |
Creates a set of (strand specific) read counts centred at the genomic features provided.
alignFeature(data, anno, offset = 1000)
data |
List with read counts as returned by |
anno |
Data frame with annotation data in GFF format. |
offset |
Half width of window around start point of annotated features. |
List with one component for each feature in anno
.
Peter Humburg
The GFF file format specification: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
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)