alignFeature {ChIPseqR} | R Documentation

## 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`.

### 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)

[Package ChIPseqR version 1.44.0 Index]