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

[Robert Castelo]

hi Hervé,

i had not imagine this could require so much code refactoring, so thanks 
a lot for the quick and extensive fix. i'll have a close look and let 
you know if i encounter any problem.

thanks again!!!

robert.

On 07/20/2017 11:23 AM, Hervé Pagès wrote:
> Hi Robert,
>
> This should work in GenomicRanges 1.29.10.
>
> Note that working on this revealed some minor shortcomings
> of the GPos internal representation so I decided to change it.
> The new one relies on IPos, a new class in IRanges 2.11.10.
> IPos is analog to GPos but for "integer positions" instead of
> "genomic positions". See ?IPos for the details.
>
> The new GPos objects behave exactly like the old ones except
> for 2 things:
>   - the strand() setter now works
>   - ranges() now returns an IPos instead of an IRanges
>     object
>
> Update any old GPos object 'x' with
>
>   x <- updateObject(x, verbose=TRUE)
>
> Let me know if you run into any issue with this.
>
> Cheers,
> H.
>
>
> On 07/18/2017 03:00 PM, Robert Castelo wrote:
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo&s=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw&e=
>>>>
>>>>
>>>>
>>>
>>
>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550