[Bioc-devel] strand<- method for 'GPos' doesn't work

[Robert Castelo]

great, thanks Hervé!

robert.

On 18/07/2017 20:57, Hervé Pagès wrote:
> Hi Robert,
>
> I'm working on this.
>
> Best,
> H.
>
> On 07/14/2017 02:31 AM, Robert Castelo wrote:
>> hi,
>>
>> the strand replacement method for 'GPos' objects does not seem to work:
>>
>> library(GenomicRanges)
>> example(GPos)
>> strand(gpos1) <- "-"
>> Error in methods::slot(object, name) :
>>    no slot of name "call" for this object of class "GPos"
>> traceback()
>> 10: methods::slot(object, name)
>> 9: getElement(x, "call")
>> 8: getCall.default(object)
>> 7: getCall(object)
>> 6: update.default(x, strand = value, check = FALSE)
>> 5: update(x, strand = value, check = FALSE)
>> 4: update(x, strand = value, check = FALSE)
>> 3: .local(x, ..., value)
>> 2: `strand<-`(`*tmp*`, value = "-")
>> 1: `strand<-`(`*tmp*`, value = "-")
>>
>> this kind of operation works perfectly on 'GRanges' objects, so i guess
>> it should also work also with 'GPos' objects:
>>
>> example(GRanges)
>> gr1
>> GRanges object with 1 range and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]     chr2 [56, 125]      *
>>    -------
>>    seqinfo: 1 sequence from an unspecified genome; no seqlength
>> strand(gr1) <- "-"
>> gr1
>> GRanges object with 1 range and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]     chr2 [56, 125]      -
>>    -------
>>    seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>
>>
>> below my session info. thanks!
>>
>> robert.
>> ps: sessionInfo()
>> sessionInfo()
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so
>> LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
>>   [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
>>   [7] LC_PAPER=en_US.UTF8       LC_NAME=C
>>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats4    stats     graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2  IRanges_2.10.2
>> [4] S4Vectors_0.14.3     BiocGenerics_0.22.0  colorout_1.1-2
>>
>> loaded via a namespace (and not attached):
>> [1] zlibbioc_1.22.0         compiler_3.4.0          tools_3.4.0
>> [4] XVector_0.16.0          GenomeInfoDbData_0.99.0 RCurl_1.95-4.8
>> [7] bitops_1.0-6
>>
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>>
>>
>