Question: zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
0
gravatar for Robert Castelo
6.0 years ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k 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
annotation polyphen sift • 780 views
ADD COMMENTlink modified 6.0 years ago by Valerie Obenchain6.7k • written 6.0 years ago by Robert Castelo2.3k
Answer: zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
0
gravatar for Valerie Obenchain
6.0 years ago by
United States
Valerie Obenchain6.7k wrote:
Hi Robert, Thanks for reporting this. Now fixed in VariantAnnotation 1.7.47. 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. 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
ADD COMMENTlink written 6.0 years ago by Valerie Obenchain6.7k
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 >
ADD REPLYlink written 6.0 years ago by Robert Castelo2.3k
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 >> >
ADD REPLYlink written 6.0 years ago by Valerie Obenchain6.7k
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 >>> >> >
ADD REPLYlink written 6.0 years ago by Robert Castelo2.3k
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