getIdeo: Download ideogram table from UCSC

In shraddhapai/IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram

Description

Download ideogram table from UCSC

Usage

getIdeo(ideoSource)

Arguments

ideoSource

(character) Genome build for data (e.g. mm10).

Details

Download table containing chromosomal extent and band locations from the UCSC genome browser Uses rtracklayer to retrieve the cytoBandIdeo. table from the UCSC genome browser. The cytoBandIdeo table contains chromosomal ideogram information and is used to graph the chromosomal bands in plotOnIdeo(). This table is provided as input to plotOnIdeo(). In the case where the user bins the data, the output of this function can also be used as input to generate bin coordinates for binning the data (see avgByBin()).

Value

(data.frame) ideogram table

See Also

avgByBin(),getBins()

Examples

getIdeo("mm9")

shraddhapai/IdeoViz documentation built on April 27, 2020, 10:36 p.m.