[BioC] Error using Homo.sapiens AnnotationDbi package with GenomicFeatures

[Chris Whelan]

Hi,

I'm having trouble using the AnnotationDbi package and was wondering
if someone could tell me what I'm doing wrong. I'm trying to use
GenomicFeatures to find promoter regions and then use AnnotationDbi to
look up the Entrez Gene IDs for those transcripts, but getting an
error. If I'm going about this all wrong let me know; I find it a
little difficult to follow the thread of the documentation of the
various feature/annotation packages. At the very least the error
message that I'm getting seems like it might be a little friendlier?

Thanks!

Chris

Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> library(GenomicFeatures)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object(s) are masked from 'package:stats':

    xtabs

The following object(s) are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
    colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

li> library(Homo.sapiens)
Loading required package: OrganismDbi
Loading required package: GO.db
Loading required package: DBI

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
> hg19UCSCGenes <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene")
Download the knownGene table ... OK
Download the knownToLocusLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... metadata: OK
> k <- elementMetadata(head(promoters(hg19UCSCGenes)))[,"tx_name"]
Warning messages:
1: In `start<-`(`*tmp*`, value = c(9874, 9874, 9874, 67091, 319084,  :
  trimmed start values to be positive
2: In `end<-`(`*tmp*`, value = c(12073, 12073, 12073, 69290, 321283,  :
  trimmed end values to be <= seqlengths
> k
[1] "uc001aaa.3" "uc010nxq.1" "uc010nxr.1" "uc001aal.1" "uc001aaq.2"
[6] "uc001aar.2"
> head(keys(Homo.sapiens, keytype="TXNAME"))
[1] "uc001aaa.3" "uc010nxq.1" "uc010nxr.1" "uc001aal.1" "uc001aaq.2"
[6] "uc001aar.2"
> select(Homo.sapiens, keys=k, keytype="TXNAME", cols=c("TXNAME", "ENTREZID")
+ )
Error in if (nrow(res) > 0L) { : argument is of length zero
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
 [1] Homo.sapiens_1.0.0
 [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
 [3] org.Hs.eg.db_2.8.0
 [4] GO.db_2.8.0
 [5] RSQLite_0.11.2
 [6] DBI_0.2-5
 [7] OrganismDbi_1.0.0
 [8] GenomicFeatures_1.10.0
 [9] AnnotationDbi_1.20.2
[10] Biobase_2.18.0
[11] GenomicRanges_1.10.4
[12] IRanges_1.16.4
[13] BiocGenerics_0.4.0
[14] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
 [1] BSgenome_1.26.1    Biostrings_2.26.2  RBGL_1.34.0        RCurl_1.95-3
 [5] Rsamtools_1.10.1   XML_3.95-0.1       biomaRt_2.14.0     bitops_1.0-4.2
 [9] graph_1.36.0       parallel_2.15.1    rtracklayer_1.18.0 stats4_2.15.1
[13] tools_2.15.1       zlibbioc_1.4.0