[Bioc-devel] seq*apply deprecation

On Wed, Jan 22, 2014 at 1:29 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:

    Hi Michael,


    On 01/12/2014 05:16 AM, Michael Lawrence wrote:

        Hi,


        It may be time to deprecate the seq*apply family of functions,
        including
        seqapply, mseqapply, tseqapply, seqby and seqsplit. These are
        ancient
        functions named in referece to the "Sequence" class, now called
        "Vector".
        It would seem better for the user to write: asList(lapply(...))
        instead of
        coming up with an alias for that. For readability, we should
        probably
        export asList() as an alias for as(x, "List"), which I just
        cleaned up.


    Sounds good to me.



        There is one caveat though: mseqapply has been particularly
        useful, because
        it delegates to mapply_List, which is smart enough to handle any
        vector
        argument in "...". The mapply,List method of course restricts
        everything to
        List. We should probably export mapply_List, probably with a
        better name.
        Suggestions?


    Why do we need all this?


Neat. Presumably due to this patch:

commit 42139699d91a34c401eedd36db62716a607d0b06
Author: maechler <maechler at 00db46b3-68df-0310-9c12-caf00c1e9a41>
Date:   Wed Nov 28 10:31:42 2012 +0000

     mapply(F, <S4>) now works thanks to a version of Herve's patch

We should do away with mapply_List now that this is part of released R.

       x <- RleList(11:14, 3:1)

    Then:

       > IRanges:::mapply_List(__function(a, b) {a+b}, x, 10)

       [[1]]
       numeric-Rle of length 4 with 4 runs
         Lengths:  1  1  1  1
         Values : 21 22 23 24

       [[2]]
       numeric-Rle of length 3 with 3 runs
         Lengths:  1  1  1
         Values : 13 12 11

    But also:

       > base::mapply(function(a, b) {a+b}, x, 10)

       [[1]]
       numeric-Rle of length 4 with 4 runs
         Lengths:  1  1  1  1
         Values : 21 22 23 24

       [[2]]
       numeric-Rle of length 3 with 3 runs
         Lengths:  1  1  1
         Values : 13 12 11

    What am I missing?

    Thanks,
    H.


        Michael

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