getCytobands {karyoploteR} | R Documentation

## getCytobands

### 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")

    #get the cytobands for Chimpanzee (not included in the package)
    cyto <- getCytobands("panTro4")

[Package karyoploteR version 1.10.5 Index]