R/getIdeo.R

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

#' Download ideogram table from UCSC
#' 
#' @details Download table containing chromosomal extent and band locations from the UCSC genome browser
#' Uses \code{rtracklayer} to retrieve the \emph{cytoBandIdeo}.
#' table from the UCSC genome browser. The \emph{cytoBandIdeo} table  
#' contains chromosomal ideogram information and is used to graph the 
#' chromosomal bands in \code{plotOnIdeo()}. This table is provided as 
#' input to \code{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 
#' \code{avgByBin()}). 
#' @usage getIdeo(ideoSource)
#' @param ideoSource (character) Genome build for data (e.g. mm10).
#' @return (data.frame) ideogram table
#' @examples getIdeo("mm9")
#' @seealso \code{avgByBin()},\code{getBins()}
#' @export
getIdeo <- function(ideoSource) {
    cytoTable <- NULL
    
    session <- browserSession();
    genome(session) <- ideoSource;
    cytoTable <- getTable(ucscTableQuery(session,"cytoBandIdeo"))
    
    return(cytoTable)
### (data.frame) ideogram table
}#, ex=function() {
#getIdeo("mm9")
#}