[BioC] error in locateVariants for a GRanges object

[Martin Morgan]

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Your devel packages are out of date, so I'd start with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>
> phone: +44.(0)207.905.2274
> [ext: 2274]
> --------------------------------------------------------------------------------
>
>
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