re:  '[BioC] question about Gviz' thread fallout:

Yesterday I rolled a relatively simple programmatic way to label UCSC
KnownGene entries with their symbols.  However, some isoforms (e.g. some
for NRIP1 and CDKN2B) seem to be missing from the mappings.

Investigating a bit, and referring to ?org.Hs.egUCSCKG, I find

...This mapping is based on the very latest build available at UCSC
   for this organism as of March 2010.  2.6 is the last release where
   you can expect it to be here.  The GenomicFeatures package
   contains functionality that replaces the need for this mapping...

Alas, I'm too thick to find where, in the TxDb or elsewhere, I could
retrieve Hugo IDs for UCSC KnownGene entries without using org.Hs.egSYMBOL.
 The latter is what I usually do:

  library(Homo.sapiens)

  txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)
  head(names(txs))
  ## [1] "1"         "10"        "100"       "1000"      "10000"
"100008586"

  names(txs) <- mget(names(txs), org.Hs.egSYMBOL, ifnotfound=NA)
  head(names(txs))
  ## [1] "A1BG"    "NAT2"    "ADA"     "CDH2"    "AKT3"    "GAGE12F"

Now, I thought for a while, hell, this gets them all!  But, not really...

  txs$NRIP1
  ## GRanges with 1 range and 2 metadata columns:
  ##       seqnames               ranges strand |     tx_id     tx_name
  ##          <Rle>            <IRanges>  <Rle> | <integer> <character>
  ##   [1]    chr21 [16333556, 16437126]      - |     71301  uc002yjx.2

Well, that's one of the isoforms.  But what about the other ones?

  org.Hs.egUCSCKG[[ "c002yjx.1" ]]
  ## NULL

  org.Hs.egUCSCKG[[ "uc010gkz.1" ]]
  ## NULL

I know UCSC identifiers can be a bit of a pain in the ass, but there do
exist mappings for these.  If they're going to be used as primary
identifiers for the TxDb packages, would it be possible to update them?

If it's an issue of time constraints, I will take a stab at it, but that
will almost guarantee more prattling from me on the mailing list.  On the
other hand, it might move GAF3.0 annotations out of the station.

Much obliged for any insights from the core developers.


-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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