[Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges
Michael Lawrence
lawrence.michael at gene.com
Thu Oct 22 03:53:42 CEST 2015
Ok, thanks. That's what R (in my working copy) basically does now. Since
internal sub-assignment is vector-based, it just calls as.vector(). That
vector may be subsequently "promoted" given the type of "x" and "value"
(like integer to real, real to character, etc). So it could be optimized,
but it was a simple change and base::ifelse() works on Rle. We should keep
the ifelse generic, with a signature on "test", so that we can dispatch on
LogicalList.
Michael
On Wed, Oct 21, 2015 at 6:38 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> On 10/21/2015 03:36 PM, Michael Lawrence wrote:
>
>> That sucks. I was thinking we could easily make R smarter about
>> sub-assignment, so that base::ifelse would just work with value Rle, as
>> would [<- in general. The C code would just call as.vector() on the
>> object. The problem is that S4 objects are seen by that code as "scalar"
>> and are wrapped in a list when sub-assigned into one:
>>
>> > l <- list()
>> > l[1] <- Rle(3:1)
>> > l
>> [[1]]
>> integer-Rle of length 3 with 3 runs
>> Lengths: 1 1 1
>> Values : 3 2 1
>>
>> But that behavior is inconsistent within the base package, because
>> lapply(), mapply() etc assume an S4 object is vector-like. I'm
>> interested in your opinion. Should we deprecate the list sub-assignment
>> behavior?
>>
>
> I think list sub-assignment should just call as.list() on the right
> value if the value is not already a list. That way base R doesn't have
> to choose whether S4 objects should be seen as "scalar" or as
> "vector-like". This decision is now in the hands of the author of the
> S4 class: if s/he chooses to have the "as.list" method for his/her
> objects to just wrap the object in a list then s/he'll get the current
> behavior (object treated as a scalar). If s/he chooses to have the
> "as.list" method return a list parallel to the object then s/he'll get
> list sub-assignment treat his/her objects as vector-like.
>
> This principle can be extended to sub-assignments in general, not just
> list sub-assignments: if the class of the right value in 'x[i] <- value'
> doesn't extend the class of 'x', then 'value' should first be coerced
> to the class of 'x':
>
> if (!is(value, class(x))
> value <- as(value, class(x))
>
> Note that this is what the "[<-" method for Vector objects (defined
> in S4Vectors) does (thru the default method for
> normalizeSingleBracketReplacementValue).
>
> Thanks,
> H.
>
>
>> Michael
>>
>>
>> On Wed, Oct 21, 2015 at 11:14 AM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>> Hi Michael,
>>
>> On 10/21/2015 07:09 AM, Michael Lawrence wrote:
>>
>> News to me. Why was this deprecated? Why can't the ifelse()
>> method just do
>> what it is now telling the user to do? Is it to make the
>> inefficiency of
>> the implementation more obvious?
>>
>>
>> There was some discussion about this here:
>>
>> https://support.bioconductor.org/p/70871/
>>
>> I should probably have brought this to bioc-devel before making that
>> change, sorry. I'll be happy to bring these methods back if there is a
>> way to preserve the semantic of base::ifelse() (which relies on
>> delayed
>> evaluation of the 'yes' and 'no' arguments).
>>
>> H.
>>
>> The goal with Rle was to make it behave as
>> conveniently and as vector-like as possible.
>>
>>
>>
>> On Wed, Oct 21, 2015 at 6:50 AM, Robert Castelo
>> <robert.castelo at upf.edu <mailto:robert.castelo at upf.edu>>
>>
>> wrote:
>>
>> hi,
>>
>> one of the recent changes in the devel IRanges has been to
>> defunct the
>> 'ifelse' method for 'Rle' objects. This was warned during
>> the previous
>> devel cycle and so it does with current release.
>>
>> One of the affected functions is the VRanges object
>> constructor,
>> 'VRanges()'. Since I use this function within my package
>> VariantFiltering,
>> this is now precluding it to build.
>>
>> I would like to ask whether you could fix the VRanges
>> constructor to
>> comply with the new requirement on the 'ifelse' method for
>> 'Rle' objects.
>>
>> please find below a reproducible example for release and
>> devel with
>> corresponding session information.
>>
>> thanks!!
>>
>> robert.
>>
>> ============================================
>>
>> This is what happens in current release:
>>
>> library(VariantAnnotation)
>>
>>
>> VRanges()
>> VRanges object with 0 ranges and 0 metadata columns:
>> seqnames ranges strand ref alt
>> totalDepth
>> refDepth altDepth sampleNames softFilterMatrix
>> <Rle> <IRanges> <Rle> <character> <characterOrRle>
>> <integerOrRle>
>> <integerOrRle> <integerOrRle> <factorOrRle> <matrix>
>> -------
>> seqinfo: no sequences
>> hardFilters: NULL
>> Warning messages:
>> 1: The "ifelse" methods for Rle objects are deprecated.
>> Please use
>>
>> as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
>>
>> instead.
>> 2: The "ifelse" methods for Rle objects are deprecated.
>> Please use
>>
>> as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
>>
>> instead.
>>
>> sessionInfo()
>> R version 3.2.2 (2015-08-14)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Fedora release 12 (Constantine)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
>> LC_TIME=en_US.UTF8
>> LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
>> [6] LC_MESSAGES=en_US.UTF8 LC_PAPER=en_US.UTF8
>> LC_NAME=C
>> LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils
>> datasets
>> methods base
>>
>> other attached packages:
>> [1] VariantAnnotation_1.16.0 Rsamtools_1.22.0
>> Biostrings_2.38.0
>> XVector_0.10.0 SummarizedExperiment_1.0.0
>> [6] Biobase_2.30.0 GenomicRanges_1.22.0
>> GenomeInfoDb_1.6.0
>> IRanges_2.4.0 S4Vectors_0.8.0
>> [11] BiocGenerics_0.16.0 vimcom_1.2-3 setwidth_1.0-4
>> colorout_1.1-0
>>
>> loaded via a namespace (and not attached):
>> [1] AnnotationDbi_1.32.0 GenomicAlignments_1.6.0
>> zlibbioc_1.16.0
>> BiocParallel_1.4.0 BSgenome_1.38.0 tools_3.2.2
>> [7] DBI_0.3.1 lambda.r_1.1.7
>> futile.logger_1.4.1
>> rtracklayer_1.30.0 futile.options_1.0.0 bitops_1.0-6
>> [13] RCurl_1.95-4.7 biomaRt_2.26.0
>> RSQLite_1.0.0
>> GenomicFeatures_1.22.0 XML_3.98-1.3
>>
>>
>>
>>
>> This is what happens in current devel:
>>
>> library(VariantAnnotation)
>>
>> VRanges()
>> Error: The "ifelse" methods for Rle objects are defunct.
>> Please use
>>
>> as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
>>
>> instead.
>> sessionInfo()
>> R Under development (unstable) (2015-10-14 r69514)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Fedora release 12 (Constantine)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
>> LC_TIME=en_US.UTF8
>> [4] LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
>> LC_MESSAGES=en_US.UTF8
>> [7] LC_PAPER=en_US.UTF8 LC_NAME=C
>> LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils
>> datasets
>> methods base
>>
>> other attached packages:
>> [1] VariantAnnotation_1.17.0 Rsamtools_1.23.0
>> Biostrings_2.39.0
>> [4] XVector_0.11.0 SummarizedExperiment_1.1.0
>> Biobase_2.31.0
>> [7] GenomicRanges_1.21.32 GenomeInfoDb_1.7.0
>> IRanges_2.5.1
>> [10] S4Vectors_0.9.2 BiocGenerics_0.17.0
>> vimcom_1.0-0
>> [13] setwidth_1.0-4 colorout_1.0-3
>>
>> loaded via a namespace (and not attached):
>> [1] AnnotationDbi_1.33.0 GenomicAlignments_1.7.0
>> zlibbioc_1.17.0
>> BiocParallel_1.5.0
>> [5] BSgenome_1.39.0 tools_3.3.0
>> DBI_0.3.1
>> lambda.r_1.1.7
>> [9] futile.logger_1.4.1 rtracklayer_1.31.0
>> futile.options_1.0.0
>> bitops_1.0-6
>> [13] RCurl_1.95-4.7 biomaRt_2.27.0
>> RSQLite_1.0.0
>> GenomicFeatures_1.23.3
>> [17] XML_3.98-1.3
>>
>> _______________________________________________
>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
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>> _______________________________________________
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>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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