[BioC] GRanges findOverlaps error
Vincent Carey
stvjc at channing.harvard.edu
Fri Oct 21 15:34:34 CEST 2011
ensure that you have current package versions and then try
updateObject() on the constituents of your call. if that doesn't work
let us know.
On Fri, Oct 21, 2011 at 7:50 AM, Kathi Zarnack <zarnack at ebi.ac.uk> wrote:
> Hi,
>
> I am using findOverlaps() to compare two GRanges objects (shown below).
> ensembl.genes was created with rtracklayer import.gff(...,genome="hg19"), so
> it contains additional information about the genome. exons was created
> manually from a list of positions etc. It seems that I can no longer compare
> the two objects which previously worked fine (I am not sure whether I
> already used this script on R-devel, but it definitely worked on R-2.13). I
> would be happy for any suggestions how to overcome this problem.
>
> Thanks for your help,
> Kathi
>
>> findOverlaps(ensembl.genes,exons)
> Error in genome(y) :
> no slot of name "genome" for this object of class "Seqinfo"
>
>> head(exons)
> GRanges with 6 ranges and 7 elementMetadata values:
> seqnames ranges strand | phase section.id
> <Rle> <IRanges> <Rle> | <numeric> <character>
> [1] chr1 [ 704549, 704591] - | 1 CUFF.1135:003
> [2] chr1 [ 764383, 764484] + | 0 CUFF.825:003
> [3] chr1 [1654546, 1654661] - | 2 CUFF.6345:097
> [4] chr1 [2303220, 2303344] - | 2 CUFF.5141:008
> [5] chr1 [3776984, 3777005] + | 1 CUFF.2849:006
> [6] chr1 [6297305, 6297405] + | 2 CUFF.3421:002
> exon.position splice.3 splice.5 ensembl.overlap ensg
> <character> <logical> <logical> <character> <logical>
> [1] terminal TRUE FALSE novel <NA>
> [2] internal TRUE TRUE any_overlap <NA>
> [3] terminal FALSE TRUE novel <NA>
> [4] internal TRUE FALSE any_overlap <NA>
> [5] terminal TRUE FALSE any_overlap <NA>
> [6] internal TRUE TRUE any_overlap <NA>
> ---
> seqlengths:
> chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX
> chrY
> NA NA NA NA NA NA ... NA NA NA NA NA
> NA
>
>> head(ensembl.genes)
> GRanges with 6 ranges and 1 elementMetadata value:
> seqnames ranges strand | ensg
> <Rle> <IRanges> <Rle> | <character>
> [1] chrX [ 99883667, 99894988] - | ENSG00000000003
> [2] chrX [ 99839799, 99854882] + | ENSG00000000005
> [3] chr20 [ 49551404, 49575092] - | ENSG00000000419
> [4] chr1 [169821804, 169863408] - | ENSG00000000457
> [5] chr1 [169631245, 169823221] + | ENSG00000000460
> [6] chr1 [ 27938575, 27961788] - | ENSG00000000938
> ---
> seqlengths:
> chr1 chr10 ... chrY
> NA NA ... NA
>
>> sessionInfo()
> R Under development (unstable) (2011-08-14 r56741)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] DEXSeq_0.1.29 Biobase_2.13.10 biomaRt_2.9.3
> [4] xtable_1.5-6 GenomicRanges_1.5.49 IRanges_1.11.30
> [7] R.utils_1.8.2 R.oo_1.8.2 R.methodsS3_1.2.1
> [10] rtracklayer_1.13.17 RCurl_1.6-10 bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.21.11 BSgenome_1.21.6 hwriter_1.3 MASS_7.3-14
> [5] plyr_1.6 stringr_0.5 tools_2.14.0 XML_3.4-3
> [9] zlibbioc_0.1.8
>>
>
> --
> Dr. Kathi Zarnack
> Luscombe Group
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD, UK
> tel +44 1223 494 526
>
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