Error in `colnames<-,ExperimentList`

[lgatto]

I am under the impression that I should be able to replace the colnames of the different assays in an ExperimentList and a MAE:

> showMethods(`colnames<-`)
Function: colnames<- (package base)
x="ANY", value="ANY"
x="CompressedSplitDataFrameList", value="ANY"
x="DataFrame", value="ANY"
x="ExperimentList", value="CompressedCharacterList"
    (inherited from: x="ANY", value="ANY")
x="ExperimentList", value="list"
    (inherited from: x="ANY", value="ANY")
x="ExperimentList", value="SimpleCharacterList"
    (inherited from: x="ANY", value="ANY")
x="matrix", value="character"
    (inherited from: x="ANY", value="ANY")
x="MultiAssayExperiment", value="list"
x="MultiAssayExperiment", value="List"
x="RangedSelection", value="ANY"
x="SimpleDataFrameList", value="ANY"
x="SummarizedExperiment", value="character"
    (inherited from: x="ANY", value="ANY")

But it doesn't work for either. Here I try with and ExperimentList

> example(SummarizedExperiment, echo = FALSE) ## to get se0
> el <- ExperimentList(list(a = se0[, 1], b = se0[, 1], c = se0[, 1]))
> el
ExperimentList class object of length 3:
 [1] a: SummarizedExperiment with 200 rows and 1 columns
 [2] b: SummarizedExperiment with 200 rows and 1 columns
 [3] c: SummarizedExperiment with 200 rows and 1 columns
> colnames(el)
CharacterList of length 3
[["a"]] A
[["b"]] A
[["c"]] A
> colnames(el) <- as.list(1:3)
Error in dimnames(x) <- dn : 'dimnames' applied to non-array
> colnames(el) <- CharacterList(as.list(1:3))
Error in dimnames(x) <- dn : 'dimnames' applied to non-array

The error is different if I try with a MAE

> mae <- MultiAssayExperiment(el)
> colnames(mae)
CharacterList of length 3
[["a"]] A
[["b"]] A
[["c"]] A
> colnames(mae) <- CharacterList(as.list(letters[1:3]))
Error in `colnames<-`(`*tmp*`, value = new("CompressedCharacterList",  : 
  'value' names and lengths should all be identical to 'names(x)'

[LiNk-NY]

Hi Laurent, @lgatto

This can be seen with :

> getMethod("colnames<-", "ExperimentList")
Error in getMethod("colnames<-", "ExperimentList") : 
  no method found for function 'colnames<-' and signature ExperimentList

The MultiAssayExperiment API does not require that all assays have a dimnames<- setter (only a getter) but I think in most cases, assay classes will have a dimnames<- method defined.

We did implement a version of this to only modify a single assay at a time. See ?renameColname.

> renameColname(mae, "a", "a") |> colnames()
CharacterList of length 3
[["a"]] a
[["b"]] A
[["c"]] A

[LiNk-NY]

Hi Laurent, @lgatto
Any updates on the issue?
Have you tried the above renameColname function?
Thanks!

[lgatto]

Hi @LiNk-NY - sorry, I have been busy with too many things to get back to that issue. I'll shortly.