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

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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

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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)