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[Bioc-devel] list() as dimnames in assayDataNew

3 messages · Benilton Carvalho, Martin Morgan

Original
Benilton Carvalho
# 
Hi,

Biobase::assayDataNew() now assigns list() as dimnames(elt) if the
original dimnames(elt) is NULL.

This is a consequence of

dimnames(elt) <- lapply(dimnames(elt), unname)

because lapply(NULL, unname) is list().

Although this works fine for regular R objects (because list() is
coerced back to NULL), this fails when elt is an ff object.

library(ff)
library(Biobase)
x = matrix(1:4, 2)
y = as.ff(x)
dimnames(x)
dimnames(y)
assayDataNew(exprs=x)
assayDataNew(exprs=y)

The documentation for dimnames()<- value states that value "can be
NULL or a list of the same length as dim(x). If a list, its components
are either NULL or a character vector with positive length of
appropriate dimension of x."

Following the strict definition of value given in the documentation
(therefore, ignoring the coercion described in Details), would you
guys consider replacing

        dimnames(elt) <- lapply(dimnames(elt), unname)

by

        dimnames(elt) <- ifelse(is.null(dimnames(elt)), NULL,
lapply(dimnames(elt), unname))

?

Thank you very much,

benilton
Martin Morgan
#
On 06/11/2012 04:42 AM, Benilton Carvalho wrote:
Hi Benilton -- I did

   if (!is.null(dimnames(elt)))
       dimnames(elt) <- lapply(dimnames(elt), unname)

in 2.17.6. Thanks for the report.

Martin

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Benilton Carvalho
    

    

      
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Thank you very much, Martin.

b

        
On 11 June 2012 22:03, Martin Morgan <mtmorgan at fhcrc.org> wrote: