humarray (version 1.2)

get.telomere.locs: Derive Telomere locations across the genome

Description

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

Usage

get.telomere.locs(dir = NULL, kb = 10, build = NULL, bioC = TRUE,
  GRanges = TRUE, text = FALSE, autosomes = FALSE, mito.zeros = 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 <=0, then this file will not be stored.

kb

The number of base pairs at the start and end of a chromosome that are defined as belonging to the telomere can be a little arbitrary. This argument allows specification of whatever threshold is required.

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.

mito.zeros

logical, Mitochondria have no telomeres (are circular) but for some purposes you might want zero values in order to match with other annotation that includes all chromosomes and MT. TRUE adds zeros for chrMT, and FALSE excludes chrMT.

Value

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

Examples

# NOT RUN {
setwd(tempdir())
get.telomere.locs()
get.telomere.locs(bioC=FALSE)
get.telomere.locs(text=TRUE)
# }