[Bioc-devel] rownames in SummerizedExperiments

When I use "mcols" on a SummerizedExperiment object, I get a DataFrame
with the row metadata, but without rownames. This is quite annoying if I
want to select specific rows using my feature identifiers.

On an arbitrary vector, the names do not need to be unique, but they DO
need to be unique on a DataFrame (according to the data.frame
conventions). Conditioning on whether there are duplicate names would be
too complicated, so it is left to the user to declare whether the names
are expected on the result. Since in general the vector names are not
valid rownames, the default is FALSE. I guess if we really wanted to be
consistent with R, we would mangle the names to make them unique, but
that check is expensive.

On Sun, Apr 6, 2014 at 2:48 PM, Simon Anders <anders at embl.de
<mailto:anders at embl.de>> wrote:

    Hi Michael

    On 06/04/14 23:32, Michael Lawrence wrote:

     > On an arbitrary vector, the names do not need to be unique, but they DO
     > need to be unique on a DataFrame (according to the data.frame
     > conventions). Conditioning on whether there are duplicate names would be
     > too complicated, so it is left to the user to declare whether the names
     > are expected on the result. Since in general the vector names are not
     > valid rownames, the default is FALSE. I guess if we really wanted to be
     > consistent with R, we would mangle the names to make them unique, but
     > that check is expensive.

    Thanks for the response, but I'm not sure I understand it. I thought
    "use.names=TRUE" instructs "mcols" to use the rownames of the
    SummerizedExperiment object as rownames for the returned DataFrame. Now,
    as the rownames of the SummerizedExperiment have to be unique anyway (at
    least, I suppose they have to -- they are names, too, after all, and not
    just an arbitrary vector), how can it happen that duplicate names might
    appear?


I don't think the SE rownames are constrained to be unique. I haven't tested it,

but I don't see the assertion in the code. This is because an SE is modeled as a
matrix, which does not have the same constraint as a data.frame.

    The use case: I have a SummerizedExperiment object with gene IDs in the
    rownames. Let's say I want to get the value in the meta-data column
    "yellowness" for "gene_D".

    With en ExpressionSet, I could write:
        fData(es)["gene_D","yellowness"]

    With SummerizeExperiment, it has to be:
        mcols(se,use.names=TRUE)["gene_D","yellowness"]

    Of course, it's no big deal, but I find it quite clumsy, and I wonder
    why it has to be this way.


Well, there's this syntax:
mcols(se["gene_D",])$yellowness


       Simon

This is because an
SE is modeled as a matrix, which does not have the same constraint as a
data.frame.

On Sat, Apr 5, 2014 at 8:42 AM, Simon Anders <anders at embl.de> wrote:

Hi

On 05/04/14 17:39, Simon Anders wrote:

When I use "mcols" on a SummerizedExperiment object, I get a DataFrame
with the row metadata, but without rownames. This is quite annoying if I
want to select specific rows using my feature identifiers.

Okay, I should have read the help page for "mcols" before posting.
Hence, I amend my question to: Is there a reason why "use.names"
defaults to FALSE?

On an arbitrary vector, the names do not need to be unique, but they DO
need to be unique on a DataFrame (according to the data.frame conventions).
Conditioning on whether there are duplicate names would be too complicated,
so it is left to the user to declare whether the names are expected on the
result. Since in general the vector names are not valid rownames, the
default is FALSE. I guess if we really wanted to be consistent with R, we
would mangle the names to make them unique, but that check is expensive.

Just for some history, as of a couple of years ago, it always copied the
names and relied on make.unique(). Herve changed it, so he might be able to
defend it better.

Michael

   Simon

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