[BioC] [devteam-bioc] getGmt error

[Martin Morgan]

On 09/06/2013 06:17 AM, Martin Morgan wrote:
>
>    txt[4694] = sub("NM_009369\t", "", txt[4694])
>    writeLines(txt, "c2.all.v4.0.orig_MODIFIED_.gmt")

maybe a better way is to avoid writing to the intermediate file

   txt = readLines("c2.all.v4.0.orig_MODIFIED_.gmt")
   ## remove duplicate entry in gene set
   txt[4694] = sub("NM_009369\t", "", txt[4694])
   getGmt(textConnection(txt))

and in this way more tightly coupling the transformation with your analysis.

Martin
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