Thanks Martin,
done, but I still get the same error.

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@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


[[alternative HTML version deleted]]




_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org<mailto:Bioconductor@r-project.org>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


--
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@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


	[[alternative HTML version deleted]]

