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

[Hervé Pagès]

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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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