humarray (version 1.0.0)

get.centromere.locs: Return Centromere locations across the genome

Description

Returns the locations of centromeres in the human genome, for a given build, as a list by chromosome, text vector, or GRanges/RangedData object.

Usage

get.centromere.locs(dir = NULL, build = NULL, bioC = TRUE, GRanges = TRUE, text = FALSE, autosomes = FALSE)

Arguments

dir

character, location to store file with the this annotation. If NULL then getOption("save.annot.in.current")>=1 will result in this file being stored in the current directory, or if

build

string, currently 'hg18' or 'hg19' to specify which annotation version to use. Default is build-36/hg-18. Will also accept integers 36,37 as alternative arguments.

bioC

logical, whether to return the annotation as a ranged S4 object (GRanges or RangedData), or as a data.frame.

GRanges

logical, whether to return a GRanges object, or FALSE to return RangedData

text

logical, whether to return locations as a text vector of the form: chrN:xxxx-xxxx

autosomes

logical, if TRUE, only return results for autosomes, if FALSE, also include X and Y.

Value

Returns a list, GRanges or RangedData object, depending on input parameters. Contained will be centromere chromosome and start and end positions.

Examples

setwd(tempdir())
get.centromere.locs()
get.centromere.locs(bioC=FALSE,autosomes=TRUE)
get.centromere.locs(text=TRUE)