bindDens2readDens: Convert a feature density into a read density

In ChIPsim: Simulation of ChIP-seq experiments

Description

Given a feature density this function produces two read densities, one for each strand.

Usage

bindDens2readDens(bindDens, fragment, nfrag = 1e+05, bind = 147, 
	minLength = 150, maxLength = 180, ...)

Arguments

bindDens	Numeric vector with the feature density for one chromosome.
fragment	Function giving the fragment length distribution.
nfrag	Number of fragments that should be simulated to generate the read distribution.
bind	Length of binding site.
minLength	Minimum fragment length.
maxLength	Maximum fragment length.
...	Further arguments to fragment.

Value

A two column matrix. The first column contains the read density for the forward strand, the second column the read density for the reverse strand.

Author(s)

Peter Humburg

See Also

feat2dens, sampleReads

Examples

set.seed(1)
## generate a (relatively short) sequence of nucleosome features
features <- placeFeatures(start=200, length=1e5)

## calculate feature density
featureDens <- feat2dens(features, length=1e5)

## convert to read density
readDens <- bindDens2readDens(featureDens, fragDens, meanLength=160) 

ChIPsim documentation built on Nov. 8, 2020, 8:09 p.m.