[BioC] error in locateVariants for a GRanges object
Martin Morgan
mtmorgan at fhcrc.org
Sat Mar 10 20:01:04 CET 2012
On 03/10/2012 10:14 AM, Lescai, Francesco wrote:
> Thanks Martin,
> done, but I still get the same error.
I can't spot the problem; maybe someone else will chime in.
(a) TxDb.Hsapiens... is still out-of-date; maybe it isn't checked by
biocLite()
(b) the error
> my.locations = locateVariants(my.ranges, txdb19)
> Error in initialize(value, ...) :
> invalid names for slots of class “RangesMatching”: matchMatrix, DIM
definitely looks like an 'old package' issue -- the RangesMatching class
was replaced by the 'Hits' class during this release cycle. It might
help to call
traceback()
after the error, and to confirm that you are accessing only functions
defined in the loaded packages by starting your R session with
R --vanilla
Obviously, the sessionInfo() needs to reflect the session the command
fails in not, e.g., R gui in one instance and the terminal in the other.
Martin
>
> My new sessionInfo is
>
>> sessionInfo()
> R Under development (unstable) (2012-01-20 r58146)
> 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] BiocInstaller_1.3.7 TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2
> [3] GenomicFeatures_1.7.30 VariantAnnotation_1.1.61
> [5] Rsamtools_1.7.38 Biostrings_2.23.6
> [7] AnnotationDbi_1.17.27 Biobase_2.15.4
> [9] GenomicRanges_1.7.33 IRanges_1.13.28
> [11] BiocGenerics_0.1.12 biomaRt_2.11.1
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.23.4 DBI_0.2-5 Matrix_1.0-4 RCurl_1.91-1 RSQLite_0.11.1
> [6] XML_3.9-4 bitops_1.0-4.1 ggplot2_0.8.9 grid_2.15.0 lattice_0.20-0
> [11] plyr_1.7.1 rtracklayer_1.15.7 snpStats_1.5.5 splines_2.15.0 survival_2.36-12
> [16] tools_2.15.0 zlibbioc_1.1.1
>
>
> On 10 Mar 2012, at 17:50, Martin Morgan wrote:
>
> On 03/10/2012 09:39 AM, Lescai, Francesco wrote:
> Hi there,
> maybe I'm just doing a silly error somewhere, but I get an error when trying to locate the variants from a GRanges object.
> I have a file with SNP positions, thefore I build up the GRanges this way
>
> my.ranges = GRanges(
> seqnames=paste("chr", my.snp.unique$chromosome, sep=""),
> IRanges(start= my.snp.unique$position,
> width=1))
>
> head(my.ranges)
> GRanges with 6 ranges and 0 elementMetadata values:
> seqnames ranges strand
> <Rle> <IRanges> <Rle>
> [1] chr1 [ 1323144, 1323144] *
> [2] chr1 [ 3544236, 3544236] *
> [3] chr1 [ 6252966, 6252966] *
> [4] chr1 [ 7861154, 7861154] *
> [5] chr1 [10425118, 10425118] *
> [6] chr1 [10502308, 10502308] *
> ---
> seqlengths:
> chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 ... chr4 chr5 chr6 chr7 chr8 chr9 chrX chrY
> NA NA NA NA NA NA NA NA NA ... NA NA NA NA NA NA NA NA
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb19<- TxDb.Hsapiens.UCSC.hg19.knownGene
> #
> my.locations = locateVariants(my.ranges, txdb19)
> Error in initialize(value, ...) :
> invalid names for slots of class “RangesMatching”: matchMatrix, DIM
>
> What am I doing wrong?
>
> Your devel packages are out of date, so I'd start with
>
> source("http://bioconductor.org/biocLite.R")
> biocLite(character())
>
> Martin
>
>
> thanks,
> Francesco
>
>
> sessionInfo()
> R Under development (unstable) (2012-01-20 r58146)
> 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_2.6.2 GenomicFeatures_1.6.7
> [3] VariantAnnotation_1.1.33 Rsamtools_1.7.27
> [5] Biostrings_2.23.6 AnnotationDbi_1.17.15
> [7] Biobase_2.15.3 GenomicRanges_1.7.16
> [9] IRanges_1.13.22 BiocGenerics_0.1.4
> [11] biomaRt_2.11.1
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.23.2 DBI_0.2-5 Matrix_1.0-3 RCurl_1.9-5 RSQLite_0.11.1
> [6] XML_3.8-0 bitops_1.0-4.1 ggplot2_0.8.9 grid_2.15.0 lattice_0.20-0
> [11] plyr_1.7.1 rtracklayer_1.15.7 snpStats_1.5.3 splines_2.15.0 survival_2.36-10
> [16] tools_2.15.0 zlibbioc_1.1.1
>
> ---------------------------------------------------------------------------------
> 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><mailto:f.lescai at ucl.ac.uk>
> phone: +44.(0)207.905.2274
> [ext: 2274]
> --------------------------------------------------------------------------------
>
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>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
>
> ---------------------------------------------------------------------------------
> 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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Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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