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sciseim/gist:69cbdb4060f2b3e19b08

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Last active August 29, 2015 14:10
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  1. @johanneswaage johanneswaage created this gist Mar 11, 2013.
    22 changes: 22 additions & 0 deletions gistfile1
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,22 @@
    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