curious behavior from VariantAnnotation 1.5.36
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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 3.6 years ago
United States
I was reannotating some discriminating loci today and found this odd case -- a site is in the 3' UTR of two transcripts for a gene, and threeUTRVariants() finds it, but AllVariants() does not. Code to reproduce the result at an example locus: packageVersion('VariantAnnotation') ## [1] '1.5.36' packageVersion('Homo.sapiens') ## [1] '1.0.0' ## test case for bioc-list: library(Homo.sapiens) library(VariantAnnotation) EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) EIF2C3.site %over% transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]] ## TRUE allVars <- locateVariants(EIF2C3.site, TxDb.Hsapiens.UCSC.hg19.knownGene, AllVariants()) length(allVars) ## 0 threePrimeVars <- locateVariants(EIF2C3.site, TxDb.Hsapiens.UCSC.hg19.knownGene, ThreeUTRVariants()) length(threePrimeVars) ## 2 Why aren't the 3' UTR matches included in the AllVariants() results? That doesn't seem like the expected behavior, at least not to me. R> sessionInfo() R Under development (unstable) (2013-02-13 r61937) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices datasets utils methods [8] base other attached packages: [1] FDb.InfiniumMethylation.hg19_1.0.6 [2] BSgenome.Hsapiens.UCSC.hg19_1.3.19 [3] BSgenome_1.27.1 [4] Homo.sapiens_1.0.0 [5] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 [6] org.Hs.eg.db_2.8.0 [7] GO.db_2.8.0 [8] RSQLite_0.11.2 [9] DBI_0.2-5 [10] OrganismDbi_1.1.13 [11] VariantAnnotation_1.5.36 [12] Rsamtools_1.11.16 [13] Biostrings_2.27.11 [14] GenomicFeatures_1.11.8 [15] AnnotationDbi_1.21.10 [16] Biobase_2.19.2 [17] chromophobe_0.50 [18] pheatmap_0.7.4 [19] ggplot2_0.9.3 [20] reshape2_1.2.2 [21] GenomicRanges_1.11.29 [22] IRanges_1.17.31 [23] BiocGenerics_0.5.6 [24] BiocInstaller_1.9.6 [25] gtools_2.7.0 [26] devtools_1.1 loaded via a namespace (and not attached): [1] biomaRt_2.15.0 bitops_1.0-5 colorspace_1.2-1 dichromat_2.0-0 [5] digest_0.6.2 evaluate_0.4.3 graph_1.37.5 grid_3.0.0 [9] gtable_0.1.2 httr_0.2 labeling_0.1 lattice_0.20-13 [13] MASS_7.3-23 Matrix_1.0-10 memoise_0.1 munsell_0.4 [17] plyr_1.8 proto_0.3-10 RBGL_1.35.0 RColorBrewer_1.0-5 [21] RCurl_1.95-3 rtracklayer_1.19.9 scales_0.2.3 stats4_3.0.0 [25] stringr_0.6.2 tcltk_3.0.0 tools_3.0.0 whisker_0.1 [29] XML_3.95-0.1 zlibbioc_1.5.0 -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 3.6 years ago
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Somehow I omitted a line... this should go immediately after library(VariantAnnotation), i.e. library(Homo.sapiens) library(VariantAnnotation) ## this following line is the one that went missing EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG)) EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) EIF2C3.site %over% transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]] ## ...the rest is as before On Wed, Feb 13, 2013 at 5:09 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > I was reannotating some discriminating loci today and found this odd case > -- a site is in the 3' UTR of two transcripts for a gene, and > threeUTRVariants() finds it, but AllVariants() does not. > > Code to reproduce the result at an example locus: > > packageVersion('VariantAnnotation') > ## [1] '1.5.36' > packageVersion('Homo.sapiens') > ## [1] '1.0.0' > > ## test case for bioc-list: > library(Homo.sapiens) > library(VariantAnnotation) > EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) > EIF2C3.site %over% > transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]] > ## TRUE > > allVars <- locateVariants(EIF2C3.site, > TxDb.Hsapiens.UCSC.hg19.knownGene, > AllVariants()) > length(allVars) > ## 0 > > threePrimeVars <- locateVariants(EIF2C3.site, > TxDb.Hsapiens.UCSC.hg19.knownGene, > ThreeUTRVariants()) > length(threePrimeVars) > ## 2 > > Why aren't the 3' UTR matches included in the AllVariants() results? > That doesn't seem like the expected behavior, at least not to me. > > > > R> sessionInfo() > R Under development (unstable) (2013-02-13 r61937) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] FDb.InfiniumMethylation.hg19_1.0.6 > [2] BSgenome.Hsapiens.UCSC.hg19_1.3.19 > [3] BSgenome_1.27.1 > [4] Homo.sapiens_1.0.0 > [5] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 > [6] org.Hs.eg.db_2.8.0 > [7] GO.db_2.8.0 > [8] RSQLite_0.11.2 > [9] DBI_0.2-5 > [10] OrganismDbi_1.1.13 > [11] VariantAnnotation_1.5.36 > [12] Rsamtools_1.11.16 > [13] Biostrings_2.27.11 > [14] GenomicFeatures_1.11.8 > [15] AnnotationDbi_1.21.10 > [16] Biobase_2.19.2 > [17] chromophobe_0.50 > [18] pheatmap_0.7.4 > [19] ggplot2_0.9.3 > [20] reshape2_1.2.2 > [21] GenomicRanges_1.11.29 > [22] IRanges_1.17.31 > [23] BiocGenerics_0.5.6 > [24] BiocInstaller_1.9.6 > [25] gtools_2.7.0 > [26] devtools_1.1 > > loaded via a namespace (and not attached): > [1] biomaRt_2.15.0 bitops_1.0-5 colorspace_1.2-1 > dichromat_2.0-0 > [5] digest_0.6.2 evaluate_0.4.3 graph_1.37.5 grid_3.0.0 > > [9] gtable_0.1.2 httr_0.2 labeling_0.1 > lattice_0.20-13 > [13] MASS_7.3-23 Matrix_1.0-10 memoise_0.1 munsell_0.4 > > [17] plyr_1.8 proto_0.3-10 RBGL_1.35.0 > RColorBrewer_1.0-5 > [21] RCurl_1.95-3 rtracklayer_1.19.9 scales_0.2.3 stats4_3.0.0 > > [25] stringr_0.6.2 tcltk_3.0.0 tools_3.0.0 whisker_0.1 > > [29] XML_3.95-0.1 zlibbioc_1.5.0 > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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Hi Tim, Thanks for reporting this. There was a typo in the method called for 3UTR's in the AllVariants() code. Now fixed in 1.5.38 and 1.4.9. library(Homo.sapiens) library(VariantAnnotation) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG)) all <- locateVariants(site, txdb, AllVariants()) three <- locateVariants(site, txdb, ThreeUTRVariants()) > identical(all, three) [1] TRUE Valerie On 02/13/2013 10:19 PM, Tim Triche, Jr. wrote: > Somehow I omitted a line... this should go immediately after > library(VariantAnnotation), i.e. > > > library(Homo.sapiens) > library(VariantAnnotation) > > ## this following line is the one that went missing > EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG)) > > EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) > EIF2C3.site %over% > transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]] > > ## ...the rest is as before > > > On Wed, Feb 13, 2013 at 5:09 PM, Tim Triche, Jr. <tim.triche at="" gmail.com="">wrote: > >> I was reannotating some discriminating loci today and found this odd case >> -- a site is in the 3' UTR of two transcripts for a gene, and >> threeUTRVariants() finds it, but AllVariants() does not. >> >> Code to reproduce the result at an example locus: >> >> packageVersion('VariantAnnotation') >> ## [1] '1.5.36' >> packageVersion('Homo.sapiens') >> ## [1] '1.0.0' >> >> ## test case for bioc-list: >> library(Homo.sapiens) >> library(VariantAnnotation) >> EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) >> EIF2C3.site %over% >> transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]] >> ## TRUE >> >> allVars <- locateVariants(EIF2C3.site, >> TxDb.Hsapiens.UCSC.hg19.knownGene, >> AllVariants()) >> length(allVars) >> ## 0 >> >> threePrimeVars <- locateVariants(EIF2C3.site, >> TxDb.Hsapiens.UCSC.hg19.knownGene, >> ThreeUTRVariants()) >> length(threePrimeVars) >> ## 2 >> >> Why aren't the 3' UTR matches included in the AllVariants() results? >> That doesn't seem like the expected behavior, at least not to me. >> >> >> >> R> sessionInfo() >> R Under development (unstable) (2013-02-13 r61937) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices datasets utils methods >> [8] base >> >> other attached packages: >> [1] FDb.InfiniumMethylation.hg19_1.0.6 >> [2] BSgenome.Hsapiens.UCSC.hg19_1.3.19 >> [3] BSgenome_1.27.1 >> [4] Homo.sapiens_1.0.0 >> [5] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 >> [6] org.Hs.eg.db_2.8.0 >> [7] GO.db_2.8.0 >> [8] RSQLite_0.11.2 >> [9] DBI_0.2-5 >> [10] OrganismDbi_1.1.13 >> [11] VariantAnnotation_1.5.36 >> [12] Rsamtools_1.11.16 >> [13] Biostrings_2.27.11 >> [14] GenomicFeatures_1.11.8 >> [15] AnnotationDbi_1.21.10 >> [16] Biobase_2.19.2 >> [17] chromophobe_0.50 >> [18] pheatmap_0.7.4 >> [19] ggplot2_0.9.3 >> [20] reshape2_1.2.2 >> [21] GenomicRanges_1.11.29 >> [22] IRanges_1.17.31 >> [23] BiocGenerics_0.5.6 >> [24] BiocInstaller_1.9.6 >> [25] gtools_2.7.0 >> [26] devtools_1.1 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.15.0 bitops_1.0-5 colorspace_1.2-1 >> dichromat_2.0-0 >> [5] digest_0.6.2 evaluate_0.4.3 graph_1.37.5 grid_3.0.0 >> >> [9] gtable_0.1.2 httr_0.2 labeling_0.1 >> lattice_0.20-13 >> [13] MASS_7.3-23 Matrix_1.0-10 memoise_0.1 munsell_0.4 >> >> [17] plyr_1.8 proto_0.3-10 RBGL_1.35.0 >> RColorBrewer_1.0-5 >> [21] RCurl_1.95-3 rtracklayer_1.19.9 scales_0.2.3 stats4_3.0.0 >> >> [25] stringr_0.6.2 tcltk_3.0.0 tools_3.0.0 whisker_0.1 >> >> [29] XML_3.95-0.1 zlibbioc_1.5.0 >> >> >> -- >> *A model is a lie that helps you see the truth.* >> * >> * >> Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >> > > >
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Hi Valerie, Thanks much for the fix! Best, --t On Thu, Feb 14, 2013 at 11:39 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > Hi Tim, > > Thanks for reporting this. There was a typo in the method called for > 3UTR's in the AllVariants() code. Now fixed in 1.5.38 and 1.4.9. > > library(Homo.sapiens) > library(VariantAnnotation) > library(TxDb.Hsapiens.UCSC.**hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.**knownGene > > site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) > EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG)) > > all <- locateVariants(site, txdb, AllVariants()) > three <- locateVariants(site, txdb, ThreeUTRVariants()) > > > identical(all, three) > [1] TRUE > > > Valerie > > > > > > On 02/13/2013 10:19 PM, Tim Triche, Jr. wrote: > >> Somehow I omitted a line... this should go immediately after >> library(VariantAnnotation), i.e. >> >> >> library(Homo.sapiens) >> library(VariantAnnotation) >> >> ## this following line is the one that went missing >> EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG)) >> >> EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) >> EIF2C3.site %over% >> transcriptsBy(TxDb.Hsapiens.**UCSC.hg19.knownGene)[[EIF2C3]] >> >> ## ...the rest is as before >> >> >> On Wed, Feb 13, 2013 at 5:09 PM, Tim Triche, Jr. <tim.triche@gmail.com>> >wrote: >> >> I was reannotating some discriminating loci today and found this odd case >>> -- a site is in the 3' UTR of two transcripts for a gene, and >>> threeUTRVariants() finds it, but AllVariants() does not. >>> >>> Code to reproduce the result at an example locus: >>> >>> packageVersion('**VariantAnnotation') >>> ## [1] '1.5.36' >>> packageVersion('Homo.sapiens') >>> ## [1] '1.0.0' >>> >>> ## test case for bioc-list: >>> library(Homo.sapiens) >>> library(VariantAnnotation) >>> EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) >>> EIF2C3.site %over% >>> transcriptsBy(TxDb.Hsapiens.**UCSC.hg19.knownGene)[[EIF2C3]] >>> ## TRUE >>> >>> allVars <- locateVariants(EIF2C3.site, >>> TxDb.Hsapiens.UCSC.hg19.**knownGene, >>> AllVariants()) >>> length(allVars) >>> ## 0 >>> >>> threePrimeVars <- locateVariants(EIF2C3.site, >>> TxDb.Hsapiens.UCSC.hg19.**knownGene, >>> ThreeUTRVariants()) >>> length(threePrimeVars) >>> ## 2 >>> >>> Why aren't the 3' UTR matches included in the AllVariants() results? >>> That doesn't seem like the expected behavior, at least not to me. >>> >>> >>> >>> R> sessionInfo() >>> R Under development (unstable) (2013-02-13 r61937) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices datasets utils methods >>> [8] base >>> >>> other attached packages: >>> [1] FDb.InfiniumMethylation.hg19_**1.0.6 >>> [2] BSgenome.Hsapiens.UCSC.hg19_1.**3.19 >>> [3] BSgenome_1.27.1 >>> [4] Homo.sapiens_1.0.0 >>> [5] TxDb.Hsapiens.UCSC.hg19.**knownGene_2.8.0 >>> [6] org.Hs.eg.db_2.8.0 >>> [7] GO.db_2.8.0 >>> [8] RSQLite_0.11.2 >>> [9] DBI_0.2-5 >>> [10] OrganismDbi_1.1.13 >>> [11] VariantAnnotation_1.5.36 >>> [12] Rsamtools_1.11.16 >>> [13] Biostrings_2.27.11 >>> [14] GenomicFeatures_1.11.8 >>> [15] AnnotationDbi_1.21.10 >>> [16] Biobase_2.19.2 >>> [17] chromophobe_0.50 >>> [18] pheatmap_0.7.4 >>> [19] ggplot2_0.9.3 >>> [20] reshape2_1.2.2 >>> [21] GenomicRanges_1.11.29 >>> [22] IRanges_1.17.31 >>> [23] BiocGenerics_0.5.6 >>> [24] BiocInstaller_1.9.6 >>> [25] gtools_2.7.0 >>> [26] devtools_1.1 >>> >>> loaded via a namespace (and not attached): >>> [1] biomaRt_2.15.0 bitops_1.0-5 colorspace_1.2-1 >>> dichromat_2.0-0 >>> [5] digest_0.6.2 evaluate_0.4.3 graph_1.37.5 grid_3.0.0 >>> >>> [9] gtable_0.1.2 httr_0.2 labeling_0.1 >>> lattice_0.20-13 >>> [13] MASS_7.3-23 Matrix_1.0-10 memoise_0.1 munsell_0.4 >>> >>> [17] plyr_1.8 proto_0.3-10 RBGL_1.35.0 >>> RColorBrewer_1.0-5 >>> [21] RCurl_1.95-3 rtracklayer_1.19.9 scales_0.2.3 >>> stats4_3.0.0 >>> >>> [25] stringr_0.6.2 tcltk_3.0.0 tools_3.0.0 whisker_0.1 >>> >>> [29] XML_3.95-0.1 zlibbioc_1.5.0 >>> >>> >>> -- >>> *A model is a lie that helps you see the truth.* >>> * >>> * >>> Howard Skipper<http: cancerres.**aacrjournals.org="" content="" 31="" 9="" **="">>> 1173.full.pdf<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.="" full.pdf=""> >>> > >>> >>> >> >> >> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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