[BioC] locateVariants - error with GRanges query?
Valerie Obenchain
vobencha at fhcrc.org
Thu Nov 29 21:29:19 CET 2012
Hi Francesco,
On 11/29/2012 06:22 AM, Lescai, Francesco wrote:
> Just to add that the same function with the same data works instead on the devel version
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 GenomicFeatures_1.9.28 AnnotationDbi_1.19.28 Biobase_2.17.6
> [5] ggbio_1.5.10 ggplot2_0.9.1 VariantAnnotation_1.3.17 Rsamtools_1.9.24
> [9] Biostrings_2.25.8 GenomicRanges_1.9.39 IRanges_1.15.24 BiocGenerics_0.3.0
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.25.3 DBI_0.2-5 Hmisc_3.9-3 MASS_7.3-19 Matrix_1.0-6 RColorBrewer_1.0-5 RCurl_1.91-1 RSQLite_0.11.1
> [9] XML_3.9-4 biomaRt_2.13.2 biovizBase_1.5.6 bitops_1.0-4.1 cluster_1.14.2 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2
> [17] grid_2.15.1 gridExtra_0.9 labeling_0.1 lattice_0.20-6 memoise_0.1 munsell_0.3 plyr_1.7.1 proto_0.3-9.2
> [25] reshape2_1.2.1 rtracklayer_1.17.14 scales_0.2.1 snpStats_1.7.3 splines_2.15.1 stats4_2.15.1 stringr_0.6 survival_2.36-14
> [33] tools_2.15.1 zlibbioc_1.3.0
>
>
The BioC packages in this devel install are from the previous devel
cycle. See http://bioconductor.org/install/ for help updating.
Here is sessionInfo() from the current devel,
> sessionInfo()
R Under development (unstable) (2012-10-26 r61028)
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 utils datasets methods
[8] base
other attached packages:
[1] VariantAnnotation_1.5.19 Rsamtools_1.11.11
Biostrings_2.27.7
[4] GenomicRanges_1.11.15 IRanges_1.17.15
BiocGenerics_0.5.1
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.21.7 Biobase_2.19.1 biomaRt_2.15.0
[4] bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5
[7] GenomicFeatures_1.11.5 RCurl_1.95-3 RSQLite_0.11.2
[10] rtracklayer_1.19.6 stats4_2.16.0 tools_2.16.0
[13] XML_3.95-0.1 zlibbioc_1.5.0
More below.
>
> On 29 Nov 2012, at 13:44, "Lescai, Francesco"<f.lescai at ucl.ac.uk<mailto:f.lescai at ucl.ac.uk>> wrote:
>
> Hi there,
> I was trying to annotate the results from an association analysis.
> I created a GRanges object and tried to annotate but I get this error
>
> loc.tdt<- locateVariants(query=tdt.top.gen, subject=txdb, region=AllVariants())
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "locateVariants", for signature "GRanges", "GRanges", "PromoterVariants"
>
> if I try to annotate just the coding variants, I don't get any error apparently but then
>
> loc.tdt<- locateVariants(query=tdt.top.gen, subject=txdb, region=CodingVariants())
> loc.tdt
> GRanges with 48 ranges and 5 metadata columns:
> Error in function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
> arguments imply differing number of rows: 9, 2
>
> The GRanges object seems ok
>
> tdt.top.gen
> GRanges with 50 ranges and 2 metadata columns:
> seqnames ranges strand | pvalue snp
> <Rle> <IRanges> <Rle> |<numeric> <factor>
> [1] chr1 [ 1581065, 1581065] + | 0.0002607 var_chr1_1581065
> [2] chr1 [112042787, 112042787] + | 0.0005042 rs35511654
> [3] chr1 [230503684, 230503684] + | 0.0002967 rs2632571
> [4] chr2 [101581508, 101581508] + | 0.0003466 rs17025086
> [5] chr2 [166740578, 166740578] + | 0.0001621 rs34701755
> [6] chr3 [ 39453057, 39453057] + | 0.0004809 rs2269349
> [7] chr3 [126219030, 126219030] + | 0.0005462 rs13072404
> [8] chr3 [142030595, 142030595] + | 0.0005320 rs78396728
> [9] chr4 [ 1388757, 1388757] + | 0.0003857 rs138170890
> ... ... ... ... ... ... ...
> ---
> seqlengths:
> chr1 chr2 chr3 chr4 chr5 chr7 ... chr10 chr11 chr16 chr19 chr20 chr22
> NA NA NA NA NA NA ... NA NA NA NA NA NA
>
> Any clue?
>
> thanks very much
> Francesco
>
>
> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.8.3
> [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
> [3] GenomicFeatures_1.9.44
> [4] AnnotationDbi_1.19.46
> [5] Biobase_2.17.8
> [6] biomaRt_2.13.2
> [7] ggbio_1.5.20
> [8] ggplot2_0.9.2.1
> [9] VariantAnnotation_1.4.5
> [10] Rsamtools_1.9.31
> [11] Biostrings_2.25.12
> [12] GenomicRanges_1.9.66
> [13] IRanges_1.15.48
> [14] BiocGenerics_0.3.2
>
> loaded via a namespace (and not attached):
> [1] biovizBase_1.5.9 bitops_1.0-4.1 BSgenome_1.25.9
> [4] cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5
> [7] dichromat_1.2-4 digest_0.5.2 grid_2.15.0
> [10] gridExtra_0.9.1 gtable_0.1.1 Hmisc_3.9-3
> [13] labeling_0.1 lattice_0.20-10 MASS_7.3-21
> [16] memoise_0.1 munsell_0.4 parallel_2.15.0
> [19] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5
> [22] RCurl_1.91-1 reshape2_1.2.1 RSQLite_0.11.2
> [25] rtracklayer_1.17.21 scales_0.2.2 stats4_2.15.0
> [28] stringr_0.6.1 tools_2.15.0 XML_3.95-0.1
> [31] zlibbioc_1.3.0
This release install has a mixture of release and devel packages. In
release BioC packages have an even 'y' and in devel they have an odd
'y'in the x.y.z version number.
Here is my session info from an updated release install,
> sessionInfo()
R version 2.15.2 RC (2012-10-24 r61009)
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
[2] GenomicFeatures_1.10.1
[3] AnnotationDbi_1.20.3
[4] Biobase_2.18.0
[5] VariantAnnotation_1.4.5
[6] Rsamtools_1.10.2
[7] Biostrings_2.26.2
[8] GenomicRanges_1.10.5
[9] IRanges_1.16.4
[10] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] biomaRt_2.14.0 bitops_1.0-5 BSgenome_1.26.1 DBI_0.2-5
[5] parallel_2.15.2 RCurl_1.95-3 RSQLite_0.11.2
rtracklayer_1.18.1
[9] stats4_2.15.2 tools_2.15.2 XML_3.95-0.1
zlibbioc_1.4.0
Let me know if you still have problems after you've updated.
Valerie
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>
> ---------------------------------------------------------------------------------
> Francesco Lescai, PhD, EDBT
> Senior Research Associate in Genome Analysis
> University College London
> Faculty of Population Health Sciences
> Dept. Genes, Development& Disease
> ICH - Molecular Medicine Unit, GOSgene team
> 30 Guilford Street
> WC1N 1EH London UK
>
> email: f.lescai at ucl.ac.uk<mailto:f.lescai at ucl.ac.uk>
> phone: +44.(0)207.905.2274
> [ext: 2274]
> --------------------------------------------------------------------------------
>
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