Get refseq genes from UCSC, and extract longest transcripts for each gene symbol

gistfile1

library("rtracklayer")
session <- browserSession("UCSC")
genome(session)<-"mm9"
query <- ucscTableQuery(session, "refGene")
tableName(query) <- "refGene"
getTable(query) -> refseq
refseq[,c(2,3,4,5,6,7,8,13)] -> refseq
refseq$"width" <- refseq$"txEnd"-refseq$"txStart"

as.character(refseq[,1]) -> refseq[,1]
as.character(refseq[,8]) -> refseq[,8]

split(refseq, refseq$"name2") -> refseqSplit

getGene <- function(x)
{
	x[which.max(x$"width"),]
}

lapply(refseqSplit, FUN=getGene) -> result
do.call("rbind", result) -> result