[BioC] GRanges findOverlaps error

[Vincent Carey]

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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