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

In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

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 <=0, then this file will not be stored.
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)

humarray documentation built on Nov. 20, 2017, 1:05 a.m.