humarray (version 1.2)

get.cyto: Return Cytoband/Karyotype locations across the genome

Description

Returns the locations of cytobands/karyotype-bands in the human genome, for a given build, as a data.frame, or GRanges/RangedData object.

Usage

get.cyto(build = NULL, dir = NULL, bioC = TRUE, GRanges = TRUE,
  refresh = FALSE)

Arguments

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.

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.

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

refresh

logical, whether to re-download the file if the existing file has become corrupted

Value

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

Examples

# NOT RUN {
require(BiocInstaller)
setwd(tempdir())
get.cyto()
cyto.frame <- get.cyto(bioC=FALSE)
prv(cyto.frame)
get.cyto(build=36)
# }