[Bioc-devel] seq*apply deprecation

[Hervé Pagès]

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?

   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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>
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-- 
Hervé Pagès

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