Hi Chris, I also noticed that in your select query from before "ENTREZID" was not coming back properly. This has now been fixed. So (after a quick update) you can also do this for the last step: res2<- select(Homo.sapiens, keys=k, cols=c("ENTREZID","TXNAME"), keytype="TXNAME") head(res2) Marc On 11/08/2012 04:44 PM, Marc Carlson wrote: > Hi Chris, > > If you load the Homo.sapiens package, you will see it load the > TxDb.Hsapiens.UCSC.hg19.knownGene package for you as a dependency. So > you don't need to call makeTranscriptDbFromUCSC(), at least not for > the track you were going for, because that was already loaded via the > TxDb.Hsapiens.UCSC.hg19.knownGene package. To get the promoter > regions, you really only need to call promoters like this: > > library(Homo.sapiens) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > proms <- promoters(txdb, upstream=2000, downstream=200) ## check the > defaults in case you don't like them! > proms > > ## Once you have the promoters, you can look up the tx_names for these > like this. > k <- proms$tx_name > > ## And then you can use select to retrieve the matching gene IDs > ## In the case of Homo.sapiens, the gene IDs actually *are* entrez > gene IDs (because that is what the knownGene track is using as a gene > ID). > res <- select(Homo.sapiens, keys=k, cols=c("GENEID","TXNAME"), > keytype="TXNAME") > head(res) > > > > Marc > > > > > On 11/08/2012 10:54 AM, Chris Whelan wrote: >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor