simpleNucCall {ChIPseqR} | R Documentation

## 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.

### Author(s)

Peter Humburg

### 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)

[Package ChIPseqR version 1.40.0 Index]