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hoardeR (version 0.10)

coverageDensity: Calculation of the coverage density

Description

Calculates the coverage density.

Usage

coverageDensity(folder, chr=c(1:22,"X","Y","MT"), chr.length=NULL,
                  posneg=FALSE, verbose=TRUE, use.sqrt=FALSE,
                  kernel.package="slideWindowSum",
                  step.size=50000, window.size=100000, bw=100)

Arguments

folder

folder with bam files

chr

Chromosome names to be plotted.

chr.length

Length of chromosome

posneg

Logical, plot pos and neg strand

verbose

Logical, verbose output

use.sqrt

Logical, apply sqrt transformation

kernel.package

Class of kernel smoother

step.size

Step size in bases

window.size

Window size in bases

bw

Bandwidth parameter

Author

Daniel Fischer

Details

This function calculates the coverage of bam-files