[Bioc-devel] RE : AnnotationDbi and select function

Hi guys,

Thanks for your feedbacks.
Indeed I put GENEID because it is used in the txdb database.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
columns(txdb)
[1] "CDSID"      "CDSNAME"    "CDSCHROM"   "CDSSTRAND"  "CDSSTART" 
 [6] "CDSEND"     "EXONID"     "EXONNAME"   "EXONCHROM"  "EXONSTRAND"
[11] "EXONSTART"  "EXONEND"    "GENEID"     "TXID"       "EXONRANK" 
[16] "TXNAME"     "TXCHROM"    "TXSTRAND"   "TXSTART"    "TXEND"    

I will move to ENTREZID which is much faster ! 
I'm glad It could help
Nicolas

________________________________________
De : bioc-devel-bounces at r-project.org [bioc-devel-bounces at r-project.org] de la part de Marc Carlson [mcarlson at fhcrc.org]
Date d'envoi : mercredi 12 mars 2014 20:18
? : bioc-devel at r-project.org
Objet : Re: [Bioc-devel] AnnotationDbi and select function

Thanks Nicolaus!  That's a good bug.  I will work on a fix.  The reason
why James work-around here functions is because the number of databases
that it has to query is fewer by one.  It is also faster for this
reason.  So when you say GENEID you mean the ids used in the associated
txdb database which means that these have to be checked against that DB
(and anything related to it extracted) and then merged with the results
of the symbol information by joining on the foreign key for these two
DBs.  So thats actually much more complex than just extracting all the
same data from just the org package even though the end result (in this
case) is the same.  The bug is probably happening in the associated
merge step.

  Marc
Hi Nicolas,

On 3/12/2014 12:39 PM, Servant Nicolas wrote:
Dear all,

I have an error using the select function from the AnnotationDbi
package.
I try to convert some geneID into Symbol, but for some strange
reasons it crashed.

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
isActiveSeq(txdb)[seqlevels(txdb)] <- FALSE
isActiveSeq(txdb)[c("chr16","chr1")] <- TRUE
geneGR <- exonsBy(txdb, "gene")
library(Homo.sapiens)
symbol <- select(Homo.sapiens, keys = names(geneGR), keytype =
"GENEID", columns = "SYMBOL")
Erreur dans head(select(Homo.sapiens, keys = names(geneGR)[1:1001],
keytype = "GENEID",  :
   erreur d'?valuation de l'argument 'x' lors de la s?lection d'une
m?thode pour la fonction 'head' : Erreur dans res[,
.reverseColAbbreviations(x, cnames), drop = FALSE] :

length(geneGR)
[1] 3269
## The first 1K work
symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1000], keytype
= "GENEID", columns = "SYMBOL")
## The 1K+1 does not !
symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype
= "GENEID", columns = "SYMBOL")
Erreur dans res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
   nombre de dimensions incorrect

It looks like I cannot convert more than 1K elements ?? Any reason
for that ?
Thank you very much
Nicolas
Not sure what 'GENEID' is in this context - it appears to be Entrez
Gene. But anyway, if you use "ENTREZID" instead, it works fine:

symbol <- select(Homo.sapiens, names(geneGR), "SYMBOL", "ENTREZID")
symbol <- select(Homo.sapiens, names(geneGR), "GENEID", "ENTREZID")
Error in res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
  incorrect number of dimensions
symbol <- select(Homo.sapiens, names(geneGR)[1:1000], "GENEID",
"ENTREZID")
symbol <- select(Homo.sapiens, names(geneGR)[1:1001], "GENEID",
"ENTREZID")
Error in res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
  incorrect number of dimensions

Best,

Jim

sessionInfo()
R Under development (unstable) (2014-03-05 r65125)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] Homo.sapiens_1.1.2
  [2] org.Hs.eg.db_2.10.1
  [3] GO.db_2.10.1
  [4] RSQLite_0.11.4
  [5] DBI_0.2-7
  [6] OrganismDbi_1.5.3
  [7] XVector_0.3.7
  [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
  [9] GenomicFeatures_1.15.9
[10] AnnotationDbi_1.25.14
[11] GenomeInfoDb_0.99.17
[12] Biobase_2.23.6
[13] GenomicRanges_1.15.32
[14] IRanges_1.21.32
[15] BiocGenerics_0.9.3
[16] RColorBrewer_1.0-5
[17] reshape2_1.2.2
[18] reshape_0.8.4
[19] plyr_1.8.1
[20] ggplot2_0.9.3.1
[21] Matrix_1.1-2-2

loaded via a namespace (and not attached):
  [1] BatchJobs_1.2             BBmisc_1.5
  [3] BiocParallel_0.5.16       biomaRt_2.19.3
  [5] Biostrings_2.31.14        bitops_1.0-6
  [7] brew_1.0-6                BSgenome_1.31.12
  [9] codetools_0.2-8           colorspace_1.2-4
[11] dichromat_2.0-0           digest_0.6.4
[13] fail_1.2                  foreach_1.4.1
[15] GenomicAlignments_0.99.29 graph_1.41.3
[17] grid_3.1.0                gtable_0.1.2
[19] iterators_1.0.6           labeling_0.2
[21] lattice_0.20-27           MASS_7.3-29
[23] munsell_0.4.2             proto_0.3-10
[25] RBGL_1.39.2               Rcpp_0.11.0
[27] RCurl_1.95-4.1            Rsamtools_1.15.32
[29] rtracklayer_1.23.15       scales_0.2.3
[31] sendmailR_1.1-2           stats4_3.1.0
[33] stringr_0.6.2             tools_3.1.0
[35] XML_3.98-1.1              zlibbioc_1.9.0

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[Bioc-devel] RE : AnnotationDbi and select function

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