getIdeo {IdeoViz} | R Documentation |
Download ideogram table from UCSC
getIdeo(ideoSource)
ideoSource |
(character) Genome build for data (e.g. mm10). |
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()
).
(data.frame) ideogram table
avgByBin()
,getBins()
getIdeo("mm9")