ChIPseqR (version 1.26.0)

simpleNucCall: Predict nucleosome positions from high-throughput sequencing data

Description

This function provides a simplified interface to callBindingSites with defaults suitable for the detection of nucleosomes.

Usage

simpleNucCall(data, bind=128, support=17, background=2000, chrLen, ...)

Arguments

data

Either an object of class AlignedRead or a list. See below for details.

bind

Length of binding region to use (see Details).

support

Length of support region to use (see Details).

background

Length of background window. If this is missing it will be set to 10*(bind+2*support).

chrLen

Numeric vector indicating the length of all chromosomes. Only needed when data is an AlignedRead object. readBfaToc may be used to supply this information.

...

Further arguments to callBindingSites

Value

A list with components

binding

A data.frame with columns ‘chromosome’, ‘position’, ‘score’ and ‘pvalue’ indicating the centre of predicted binding sites together with their score and associated p-value.

score

A list with all calculated scores. One numeric vector per chromosome.

pval

A list with all corrected p-values. One numeric vector per chromosome.

References

~put references to the literature/web site here ~

See Also

callBindingSites for additional parameters.

Examples

## generate some simple artificial read data
set.seed(1)

## determine binding site locations
b <- sample(1:1e6, 5000)

## 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), 50000))
rev <- c(rev, sample(25:1e6, 50000))

## 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(150000, 150000))))

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

## predict binding site locations
bindScore <- simpleNucCall(readPile, bind=147, support=20, plot=FALSE)