#' Get array platform annotation for probes
#'
#' @param geo.id GEO id.
#' @param probe.conversion Id of the column used for probe gene mapping.
#' @param output.dir Directory to store files.
#' @return Data frame containing gene mapping.
#' @keywords internal
get.platform.annotation<-function(geo.id, probe.conversion, output.dir) {
data.set = get.data.set(geo.id, output.dir, is.annotation=T)
d = GEOquery::Table(data.set)
#print(colnames(d))
#print(probe.conversion)
#print(length(d[,probe.conversion]))
gene.mapping = data.frame(Probe = d[,"ID"], Gene = d[,probe.conversion]) #row.names = d[,"ID"], "Gene.Symbol",
return(gene.mapping)
# Alternative using bioconductor annotation packages
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("hgu133a")
#mget("121_at",hgu133aSYMBOL)
#mget("121_at",hgu133aUNIGENE)
}
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