coverageDensity: Calculation of the coverage density

In fischuu/hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

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

Details

This function calculates the coverage of bam-files

Author(s)

Daniel Fischer

fischuu/hoardeR documentation built on April 13, 2024, 1:20 p.m.