This is great news, thanks Valerie!! best regards, robert. On 9/24/13 9:17 PM, Valerie Obenchain wrote: > I will update the SIFT and PolyPhen databases for the upcoming release. > > Valerie > > > On 09/23/2013 02:21 PM, Robert Castelo wrote: >> hi Valerie, >> >> On 9/23/13 9:41 PM, Valerie Obenchain wrote: >>> Hi Robert, >>> >>> Thanks for reporting this. Now fixed in VariantAnnotation 1.7.47. >>> >> great! thanks for the quick fix. >> >>> Have you looked at the ensemblVEP package? It's a wrapper to Ensembl's >>> Variant Effect Predictor tool. We encourage the use of ensemblVEP >>> instead of the SIFT and PolyPhen databases because it accesses the >>> most current information. As you know, the SIFT and PolyPhen dbs are >>> becoming dated and we don't have plans to package newer versions. >>> >>> emsemblVEP requires that you download and install the script located >>> here, >>> >>> http://uswest.ensembl.org/info/docs/tools/vep/script/vep_download.html >>> >>> The variant_effect_predictor.pl executable must be in your path. Let >>> us know if you have trouble with the install/setup. >> yes, i looked at it, and i think it is a great solution for analysis of >> a few hundred variants as it needs to acces the internet to download the >> information. However, i'm working on a package that eventually needs to >> annotate a few thousand variants and i find the dependency on an >> external perl script that the end user must install, somewhat troubling. >> let me know if you have suggestions about this. >> >> for software packages that need to efficiently access SIFT and PolyPhen >> annotations from R, freezing the data regularly is, in my opinion, a >> much better solution. i was actually going to ask you if you could >> update these two packages. As much as you want to keep an up to date >> version of the SNPloc.Hsapiens.* or TxDb.* packages, i'd do it for SIFT >> and Polyphen, unless there's some licensing issue that prevents this, as >> it happens now with OMIM. >> >> cheers, >> robert. >> >>> Valerie >>> >>> On 09/20/2013 05:25 PM, Robert Castelo wrote: >>>> Dear list, >>>> >>>> interrogating the TxDb.Hsapiens.UCSC.hg19.knownGene package with no >>>> result gives the following expected result: >>>> >>>> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >>>> select(TxDb.Hsapiens.UCSC.hg19.knownGene, keys="dummy", >>>> keytype="GENEID", cols="SYMBOL") >>>> [1] GENEID >>>> <0 rows> (or 0-length row.names) >>>> >>>> however, when i try the same with the annotation packages >>>> PolyPhen.Hsapiens.dbSNP131 and SIFT.Hsapiens.dbSNP132, the select >>>> instruction breaks into an error: >>>> >>>> library(SIFT.Hsapiens.dbSNP132) >>>> library(PolyPhen.Hsapiens.dbSNP131) >>>> >>>> select(SIFT.Hsapiens.dbSNP132, keys=c("dummy")) >>>> Error in data.frame(RSID = unlist(rsid), PROTEINID = >>>> unlist(protein_id), : >>>> arguments imply differing number of rows: 1, 0 >>>> >>>> select(PolyPhen.Hsapiens.dbSNP131, keys="dummy") >>>> Error in `*tmp*`$RSID : $ operator is invalid for atomic vectors >>>> >>>> i guess these two annotation packages should work analogously to >>>> TxDb.Hsapiens.UCSC.hg19.knownGene, and give just a 0-row data.frame >>>> object, right? >>>> >>>> these errors reproduce also with the current devel version of BioC, >>>> please find below both sessionInfo() outputs. >>>> >>>> cheers, >>>> robert. >>>> >>>> =====RELEASE==== >>>> R version 3.0.1 (2013-05-16) >>>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets >>>> methods base >>>> >>>> other attached packages: >>>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 GenomicFeatures_1.12.3 >>>> [3] AnnotationDbi_1.22.6 Biobase_2.20.1 >>>> [5] PolyPhen.Hsapiens.dbSNP131_1.0.2 SIFT.Hsapiens.dbSNP132_1.0.2 >>>> [7] RSQLite_0.11.4 DBI_0.2-7 >>>> [9] VariantAnnotation_1.6.7 Rsamtools_1.12.4 >>>> [11] Biostrings_2.28.0 GenomicRanges_1.12.5 >>>> [13] IRanges_1.18.3 BiocGenerics_0.6.0 >>>> [15] vimcom_0.9-8 setwidth_1.0-3 >>>> [17] colorout_1.0-0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] biomaRt_2.16.0 bitops_1.0-6 BSgenome_1.28.0 >>>> RCurl_1.95-4.1 rtracklayer_1.20.4 >>>> [6] stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 zlibbioc_1.6.0 >>>> >>>> >>>> >>>> =====DEVEL===== >>>> R version 3.0.1 (2013-05-16) >>>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets >>>> methods base >>>> >>>> other attached packages: >>>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 GenomicFeatures_1.13.40 >>>> [3] AnnotationDbi_1.23.23 Biobase_2.21.7 >>>> [5] PolyPhen.Hsapiens.dbSNP131_1.0.2 SIFT.Hsapiens.dbSNP132_1.0.2 >>>> [7] RSQLite_0.11.4 DBI_0.2-7 >>>> [9] VariantAnnotation_1.7.46 Rsamtools_1.13.41 >>>> [11] Biostrings_2.29.19 GenomicRanges_1.13.44 >>>> [13] XVector_0.1.4 IRanges_1.19.37 >>>> [15] BiocGenerics_0.7.5 vimcom_0.9-8 >>>> [17] setwidth_1.0-3 colorout_1.0-0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] biomaRt_2.17.3 bitops_1.0-6 BSgenome_1.29.1 >>>> RCurl_1.95-4.1 rtracklayer_1.21.12 >>>> [6] stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 >>>> zlibbioc_1.7.0 >>>> >>>> _______________________________________________ >>>> 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 >>> >> >