SomatiCA (version 2.2.0)

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

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.

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)