[Bioc-devel] rbind for ExpressionSet objects?
The idea is for rbind2 and cbind2 to be able to deal with multiple arguments by combining them pairwise, where there is some chance of dealing with the ambiguity. There are some notes in the man page, and use of these in a non-trivial way requires buying into a number of other things that one may or may not want to do (and some care may be needed to turn this on and off in appropriate situations). ETH-Martin, while I understand your desire to make rbind2 etc some sort of standard for S4, as FHCRC-Martin said, that is not the operation that is being performed (at least not very often). We typically have much more complex arrangments (and in a sense this would be more like merge and friends, but still different enough that I think we need to keep our notion of combine.
Martin Morgan wrote:
I guess another difference between rbind / cbind / combine and rbind2 / cbind2 is that the latter only allow for two arguments (perhaps that is what the '2' is for?) whereas the former will do their work on any number of arguments. Martin Martin Maechler <maechler at stat.math.ethz.ch> writes:
"GS" == Gordon K Smyth <smyth at wehi.edu.au>
on Thu, 1 May 2008 10:26:01 +1000 (E. Australia Standard Time) writes:
GS> Hi Martin,
GS> I have only just noticed that the methods package now has generic
GS> functions rbind2() and cbind2(), which it didn't when the combine()
GS> function was first created for Biobase.
GS> I think it would be clearer and more elegant to implement rbind2() and
GS> cbind2() methods for ExpressionSet, and to retire combine() sometime down
GS> the track (not obviously for the imminent Bioconductor release). The term
GS> "combine" is a somewhat overused, e.g., it conflicts with the c() function
GS> in base.
GS> What do you think?
(I'm another 'Martin' but nevertheless .. : )
I'm strongly in favor of providing rbind2() and cbind2()
methods, base combine() on these for now, and deprecate
combine().
rbind2() and cbind2() had been introduced exactly for the
purpose of providing rbind() / cbind() - like methods for S4
objects.
Martin Maechler, ETH Zurich
GS> Cheers
GS> Gordon
GS> On Fri, 4 Apr 2008, Martin Morgan wrote:
>> Thanks for the suggestion and examples.
>>
>> I implemented this in Biobase 1.99.5. It is slightly different from the
>> version in the beadarraySNP package, in that the content of overlapping
>> regions of the exprs arrays have to be identical (beadarraySNP allows NAs in
>> the second matrix).
>>
>> The functionality I implemented is consistent with the following tests
>> (hopefully self-explanatory).
>>
>> data(sample.ExpressionSet)
>> obj <- sample.ExpressionSet
>>
>> checkEquals(obj, combine(obj[1:250,], obj[251:500,]))
>> checkEquals(obj, combine(obj[,1:13], obj[,14:26]))
>> ## overlapping
>> checkEquals(obj, combine(obj[1:300,], obj[250:500,]))
>> checkEquals(obj, combine(obj[,1:20], obj[,15:26]))
>>
>>
>> The implementation introduces a combine method for matricies, which is
>> consistent with these tests:
>>
>> ## dimnames
>> m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4]))
>> checkEquals(m, combine(m, m))
>> checkEquals(m, combine(m[1:3,], m[4:5,]))
>> checkEquals(m, combine(m[,1:3], m[,4, drop=FALSE]))
>> ## overlap
>> checkEquals(m, combine(m[1:3,], m[3:5,]))
>> checkEquals(m, combine(m[,1:3], m[,3:4]))
>> checkEquals(matrix(c(1:3, NA, NA, 6:8, NA, NA,
>> 11:15, NA, NA, 18, NA, NA),
>> nrow=5,
>> dimnames=list(LETTERS[1:5], letters[1:4])),
>> combine(m[1:3,1:3], m[3:5, 3:4]))
>> ## row reordering
>> checkEquals(m[c(1,3,5,2,4),], combine(m[c(1,3,5),], m[c(2,4),]))
>> ## Exceptions
>> checkException(combine(m, matrix(0, nrow=5, ncol=4)),
>> silent=TRUE) # types differ
>> checkException(combine(m, matrix(0L, nrow=5, ncol=4)),
>> silent=TRUE) # attributes differ
>> m1 <- matrix(1:20, nrow=5)
>> checkException(combine(m, m1), silent=TRUE) # dimnames required
>>
>> Please let me know if you had something else in mind, or if there are
>> problems with this.
>>
>> Martin
>>
>> Laurent Gautier wrote:
>>> That would be useful.
>>>
>>> I have been in a situation where it would have been useful, and spent some
>>> time
>>> with combine as well before writing my own ad-hoc solution.
>>>
>>>
>>>
>>> Laurent
>>>
>>>
>>> 2008/4/4, Gordon K Smyth <smyth at wehi.edu.au>:
>>>> An rbind() method or an rbind-like function for ExpressionSet objects
>>>> would be useful. Any plans for such a function?
>>>>
>>>> At the moment, an ExpressionSet object can be subsetted by rows or
>>>> columns. Column subsets can be put back together using combine(), but
>>>> there's no way I think to put row subsets back together.
>>>>
>>>> BTW, the help page for the generic function combine() includes the idea
>>>> of
>>>> combining by rows, but this concept is not honoured by the combine method
>>>> for the eSet class.
>>>>
>>>> Cheers
>>>> Gordon
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>>
GS> _______________________________________________
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GS> https://stat.ethz.ch/mailman/listinfo/bioc-devel
Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org