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[Bioc-devel] rbind for ExpressionSet objects?

4 messages · Gordon K Smyth, Laurent Gautier, J.Oosting at lumc.nl +1 more

Original
Gordon K Smyth
# 
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
Laurent Gautier
# 
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>:

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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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: