[Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats
Hervé Pagès
hpages at fredhutch.org
Fri Apr 7 07:26:28 CEST 2017
Hi Maarten, Vince,
We need to fix this. The plan is to promote rowRanges to an S4 generic
in the DelayedArray package (DelayedArray depends on matrixStats). And
to remove the rowRanges S4 generic defined in SummarizedExperiment
(SummarizedExperiment depends on DelayedArray). So we'll have only 1
rowRanges generic (defined in DelayedArray). With methods defined in
matrixStats (default method), DelayedArray (method for DelayedMatrix
objects), and SummarizedExperiment (method for
RangedSummarizedExperiment objects).
Then there won't be anymore conflict.
Will fix this ASAP.
H.
On 04/06/2017 03:11 AM, Vincent Carey wrote:
> I am sure there are better responses to come, but here are a few initial
> comments.
>
> On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson <mviterson at gmail.com>
> wrote:
>
>> Dear all,
>>
>> SummarizedExperiment and matrixStats both contain a method/function called
>> rowRanges one operates on a SummarizedExperiment-object the other on a
>> matrix. matrixStats is required by SummarizedExperiment, or a package it is
>> depending on, so rowRanges is masked when loading SummarizedExperiment.
>>
>> I thought a function/method is called depended on the type of the object;
>>
>
> There are at least two interpretations of this. If a function that is an
> S3 generic is called on an entity whose class corresponds to an existing
> method, that method will be invoked. If a function that is an S4 generic
> is called with (a sequence of) arguments corresponding to a method with
> signature equivalent to the sequence of classes of the arguments, that
> method will be invoked. In matrixStats, rowRanges is just a first level
> function, and will be invoked directly on anything that is passed -- e.g.,
> rowRanges(4) is just an error, when matrixStats alone is loaded.
>
> matrix or SummarizedExperiment-object, such that functions/methods with the
>> same name can coexist. However, this doesn't seems to work for rowRanges.
>> The only way to access rowRanges from matrixStats when SummarizedExperiment
>> is already loaded is using the double colon operator
>> matrixStats::rowRanges. Is this intentional or is there a other way to
>> solve this?
>>
>> Regards,
>> Maarten
>>
>> Here is a small example showing the issue:
>>
>>> library(SummarizedExperiment)
>> Loading required package: matrixStats
>> matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for
>> help.
>> Attaching package: ‘matrixStats’
>> Attaching package: ‘SummarizedExperiment’
>> The following object is masked from ‘package:matrixStats’:
>> rowRanges
>>> nrows <- 200; ncols <- 6
>>> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
>>> rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
>> + IRanges(floor(runif(200, 1e5, 1e6)), width=100),
>> + strand=sample(c("+", "-"), 200, TRUE),
>> + feature_id=sprintf("ID%03d", 1:200))
>>> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
>> + row.names=LETTERS[1:6])
>>> rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
>> + rowRanges=rowRanges, colData=colData)
>>>
>>> rowRanges(rse)
>> GRanges object with 200 ranges and 1 metadata column:
>> seqnames ranges strand | feature_id
>> <Rle> <IRanges> <Rle> | <character>
>> [1] chr1 [858613, 858712] - | ID001
>>>
>>> rowRanges(counts)
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function ‘rowRanges’ for signature
>> ‘"matrix"’
>>>
>>> library(matrixStats) ##it is already loading so this doesn't alter the
>>
>
> Actually in this case matrixStats is loaded and attached. Sometimes the
> difference is significant.
>
>
>> search path
>>>
>>> rowRanges(rse)
>> GRanges object with 200 ranges and 1 metadata column:
>> seqnames ranges strand | feature_id
>> <Rle> <IRanges> <Rle> | <character>
>> [1] chr1 [858613, 858712] - | ID001
>>> rowRanges(counts)
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function ‘rowRanges’ for signature
>> ‘"matrix"’
>>
>
> So -- we got a warning when there was a collision in namespaces, when
> SummarizedExperiment was attached, and an indication that rowRanges is an
> S4 generic when we encountered the error. When should we introduce
> the method
>
> setMethod("rowRanges", "matrix", function(x, ...) matrixStats::rowRanges(x,
> ...))
>
> that would foster the behavior I think you are looking for?
>
>
>>
>>> head(matrixStats::rowRanges(counts))
>> [,1] [,2]
>> [1,] 51.27791 9350.048
>> [2,] 1417.41010 8272.040
>>> sessionInfo()
>> R Under development (unstable) (2016-08-25 r71150)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 14.04.5 LTS
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats4 stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] SummarizedExperiment_1.5.7 DelayedArray_0.1.7
>> [3] matrixStats_0.51.0 Biobase_2.35.1
>> [5] GenomicRanges_1.27.23 GenomeInfoDb_1.11.10
>> [7] IRanges_2.9.19 S4Vectors_0.13.15
>> [9] BiocGenerics_0.21.3
>>
>> loaded via a namespace (and not attached):
>> [1] lattice_0.20-34 bitops_1.0-6 grid_3.4.0
>> [4] zlibbioc_1.21.0 XVector_0.15.2 Matrix_1.2-8
>> [7] RCurl_1.95-4.8 GenomeInfoDbData_0.99.0
>>
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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
Phone: (206) 667-5791
Fax: (206) 667-1319
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