[Bioc-devel] seq*apply deprecation

Hi Michael,
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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[Bioc-devel] seq*apply deprecation

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