combineCols should keep names in metadata with use.names=TRUE

[LTLA]

I'm not quite sure why I did this, but the current code at

SummarizedExperiment/R/combine-methods.R

Line 244 in 8df9772

metadata=unlist(lapply(all.se, metadata), recursive=FALSE, use.names=FALSE),

wipes out the names of the metadata list, e.g.,

example(SummarizedExperiment, verbose=FALSE)
metadata(se) <- list(A=1, B=2, C=3)
rownames(se) <- seq_len(nrow(se))
combined <- combineCols(se, se)
metadata(combined)
## [[1]]
## [1] 1
## 
## [[2]]
## [1] 2
## 
## [[3]]
## [1] 3
## 
## [[4]]
## [1] 1
## 
## [[5]]
## [1] 2
## 
## [[6]]
## [1] 3

Oops. Same issue affects both SEs and RSEs at their respective methods.

It should be easily fixable by just doing something like this:

all.meta <- lapply(all.se, metadata)
names(all.meta) <- NULL # or unname, I suppose
combined.meta <- unlist(all.meta, recursive=FALSE)

And then using that in the args list. This eliminates the names from the argument list of combineCols(...), while preserving the list names inside the metadata() for each SE. This gives a relatively nicer:

metadata(combined)
## $A
## [1] 1
## 
## $B
## [1] 2
## 
## $C
## [1] 3
## 
## $A
## [1] 1
## 
## $B
## [1] 2
## 
## $C
## [1] 3

Duplicate names... oh well, we'll just have to put up with it.