getCytobands: getCytobands

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Get the cytobands of the specified genome.

Usage

getCytobands(genome="hg19", use.cache=TRUE)

Arguments

genome	(character or other) specifies a genome using the UCSC genome name. Defaults to "hg19". If it's not a character, genome is ignored and and empty GRanges is returned.
use.cache	(boolean) wether to use or not the cytoband information included in the packge. use.cache=FALSE will force a download from the UCSC.

Details

It returns GRanges object with the cytobands of the specified genome. The cytobands for some organisms and genome versions have been pre-downloaded from UCSC and included in the karyoploteR package. For any other genome, getCytobands will use rtracklayer to try to fetch the cytoBandIdeo table from UCSC. If for some reason it is not possible to retrieve the cytobands, it will return an empty GRanges object. Setting the parameter use.cache to FALSE, the data included in the package will be ignored and the cytobands will be downloaded from UCSC.

The genomes (and versions) with pre-downloaded cytobands are: hg19, hg38, mm9, mm10, rn5, rn6, danRer10, dm6, ce6 and sacCer3.

Value

It returns a GenomicRanges object with the cytobands of the specified genome. If no cytobands are available for any reason, an empty GRanges is returned.

Note

This function is memoised (cached) using the memoise package. To empty the cache, use forget(getCytobands)

See Also

plotKaryotype

Examples

 
#get the cytobands for hg19 (using the data included in the package)
cyto <- getCytobands("hg19")

#do not use the included data and force the download from UCSC
cyto <- getCytobands("hg19", use.cache=FALSE)

#get the cytobands for Drosophila Melanogaster
cyto <- getCytobands("dm6")

 

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.