[Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

[Vincent Carey]

On Mon, Sep 22, 2014 at 10:17 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> >
> https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
>  >
>  >shows some modifications to [ that allow subsetting of SE by
>  >gene or pathway name
>
> Without reading the code, do you intend that SE[i,j]  will , if i is
> provided as vector of string, will subset those rows where the name of the
> GRanges == i?
>
>
By 'the GRanges' do you mean rowData(SE)?

My code breaks that capability -- e.g.,  ALLse["982_at",] now fails.
But I think that could be handled if desired.


> >it may be premature to work at the [ level.  Kasper suggested defining
>  >a suite of subsetBy operations that would accomplish this
>
> Reminder of a little background to where we are now,  with warnings of
> lurking dragons:
>
>
Thanks for the reminder.  I understand that training dragons can cause
tears to be shed.


> http://thread.gmane.org/gmane.science.biology.informatics.conductor/52971/focus=52993
>
>  >
>  >i think we could get something along these lines into the release without
>  >too much more work.  votes?
>  >
> Abstaining for now.
>
> Thanks - the topic is dear to me too.
>

	[[alternative HTML version deleted]]