[BioC] problem with TXNAME -> SYMBOL mapping in Homo.sapiens library

[Aleksandra Pfeifer [guest]]

Hello,
  I have a problem with the maping from txname to symbol of the gene. For most transcripts it works ok, but for some it doesn't:

> library(Homo.sapiens)
> select(Homo.sapiens, cols="SYMBOL", keys= "uc021wml.1", keytype="TXNAME")
Error in .testIfKeysAreOfProposedKeytype(x, keys, keytype) :
  None of the keys entered are valid keys for the keytype specified.

The traceback is as follows:
> traceback()
10: stop("None of the keys entered are valid keys for the keytype specified.")
9: .testIfKeysAreOfProposedKeytype(x, keys, keytype)
8: .select(x, keys, cols, keytype, jointype = jointype)
7: .local(x, keys, cols, keytype, ...)
6: select(.makeReal(nodeName), keys = fromKeys, cols = needCols[[nodeName]],
       keytype = toKey)
5: select(.makeReal(nodeName), keys = fromKeys, cols = needCols[[nodeName]],
       keytype = toKey)
4: .getSelects(x, keytype, keys, needCols, visitNodes)
3: .select(x, keys, cols, keytype, ...)
2: select(Homo.sapiens, cols = "SYMBOL", keys = "uc021wml.1", keytype = "TXNAME")
1: select(Homo.sapiens, cols = "SYMBOL", keys = "uc021wml.1", keytype = "TXNAME")


However, When I try to check whether the problematic txname is present in Homo.sapiens database, it occurs that it is there. I can also find some other information about this transcript:
> "uc021wml.1" %in% keys(Homo.sapiens, keytype="TXNAME")
[1] TRUE
> select(Homo.sapiens, cols="TXSTART", keys= "uc021wml.1", keytype="TXNAME")
      TXNAME  TXSTART
1 uc021wml.1 22385572

Is there a way to solve that problem? I would be appreciated for your help.

Best regards,
Aleksandra Pfeifer



 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] Homo.sapiens_1.1.1
 [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
 [3] org.Hs.eg.db_2.9.0
 [4] GO.db_2.9.0
 [5] RSQLite_0.11.4
 [6] DBI_0.2-7
 [7] OrganismDbi_1.2.0
 [8] GenomicFeatures_1.12.4
 [9] GenomicRanges_1.12.5
[10] IRanges_1.18.4
[11] AnnotationDbi_1.22.6
[12] Biobase_2.20.1
[13] BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] BSgenome_1.28.0    Biostrings_2.28.0  RBGL_1.36.2        RCurl_1.95-4.1
 [5] Rsamtools_1.12.4   XML_3.98-1.1       biomaRt_2.16.0     bitops_1.0-6
 [9] graph_1.38.3       rtracklayer_1.20.4 stats4_3.0.1       tools_3.0.1
[13] zlibbioc_1.6.0
>


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