[Bioc-devel] names, mcols and metadata are not changed in "[<-" operator of class Vector

[Hervé Pagès]

Hi Sebastian,

This is the expected behavior and it's motivated by how [<- behaves on
ordinary vectors:

   x <- setNames(1:3, LETTERS[1:3])

Then:

   > x
   A B C
   1 2 3

Replacing the first two elements:

   x[2:1] <- x[1:2]

Then:

   > x
   A B C
   2 1 3

The names are preserved.

So we need to think of [<- as an operator that touches the values of
a vector-like object without touching its structure or its attributes.
People sometimes rely on this behavior to stuff the entire object with
a given value:

   x[] <- some_value

They wouldn't expect this to destroy the names or metadata cols that
are on 'x'.

Hope that makes sense,

Cheers,
H.


On 05/07/2014 11:59 AM, Sebastian Gibb wrote:
> Dear all,
>
> today I observed an unexpected behaviour (at least for me) using the "[<-"
> operator on classes that inherited "Vector".
> I want to change the order of some elements inside the Vector (in my use case it
> is an AAStringSet object). If I use an index in "[<-" the names, the
> elementMetadata and the metadata are not replaced by their counterparts, e.g.:
>
> ###
> library("IRanges")
>
> i <- IRanges(1:3, 4:6)
> names(i) <- LETTERS[1:3]
>
> i
> # IRanges of length 3
> #     start end width names
> # [1]     1   4     4     A
> # [2]     2   5     4     B
> # [3]     3   6     4     C
>
> i[2:1] <- i[1:2]
> i
> # IRanges of length 3
> #     start end width names
> # [1]     2   5     4     A
> # [2]     1   4     4     B
> # [3]     3   6     4     C
>
>
> ## names should be B, A, C; the elementMetadata and metadata are in the wrong
> ## order, too.
> ## expected output:
> # IRanges of length 3
> #     start end width names
> # [1]     2   5     4     B
> # [2]     1   4     4     A
> # [3]     3   6     4     C
>
> ###
>
> I tried to figure out the reason for this and ended up with the "replaceROWS"
> method (in {IRanges,S4Vectors}/R/Vector-class.R).
> In this method the mcols, metadata and names are just restored. To be honest I
> do not really understand this function.
> Why is the new value first append to the original vector (`ans <- c(x, value)`)
> and subsequently extracted? Would a simple replace, e.g. `x[i] <- value` not be
> enough?
>
> In my opinion the last three lines should restore the original metadata
> *and* replace the corresponding metadata by their new counterparts.
>
> ### replaceROWS from IRanges/R/Vector-class.R
> setMethod("replaceROWS", "Vector",
>      function(x, i, value)
>      {
>          idx <- seq_along(x)
>          i <- extractROWS(setNames(idx, names(x)), i)
>          ## Assuming that objects of class 'class(x)' can be combined with c().
>          ans <- c(x, value)
>          idx[i] <- length(x) + seq_len(length(value))
>          ## Assuming that [ works on objects of class 'class(x)'.
>          ans <- ans[idx]
>          ## Restore the original decoration.
>          metadata(ans) <- metadata(x)
>          names(ans) <- names(x)
>          mcols(ans) <- mcols(x)
>          ans
>      }
> )
> ###
>
> Kind regards,
>
> Sebastian
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
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