GCcount: Calculate the GC content of given window size for a...

In SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

Description

The function downloads the .fa.gz of a given chromosome from UCSC genome browser and calculate the GC content for given window size.

Usage

GCcount(chr, binsize, url)

Arguments

chr	chromosome name. e.g. "chr1".
binsize	window size. e.g. 1000000.
url	diretory of human genome assembly. e.g."http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/".

Value

A GRanges object.

chr	A character vector. Chromosome information.
interval1	An integer vector. Start position of each bin.
interval2	An integer vector. End position of each bin.
GC	A numeric vector. GC content of each bin.

Author(s)

Mengjie Chen

Examples

chr <- "chr1"
url <- "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/"
#downloding speed may depend on the machine and internet
#test <- GCcount(chr, 10000, url)

SomatiCA documentation built on Oct. 5, 2016, 4:18 a.m.