[Bioc-devel] rbind for ExpressionSet objects?
mtmorgan at fhcrc.org
Sat Apr 5 02:21:51 CEST 2008
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
obj <- sample.ExpressionSet
checkEquals(obj, combine(obj[1:250,], obj[251:500,]))
checkEquals(obj, combine(obj[,1:13], obj[,14:26]))
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:
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]))
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),
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),]))
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.
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.
> 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.
>> Bioc-devel at stat.math.ethz.ch mailing list
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