[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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