Tim Triche, Jr. | 14 Feb 02:09 2013
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curious behavior from VariantAnnotation 1.5.36

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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