On 01/22/2014 03:02 PM, Michael Lawrence wrote:
On Wed, Jan 22, 2014 at 1:29 PM, Hervé Pagès <hpa...@fhcrc.org
<mailto:hpa...@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@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.
Furthermore, maybe she should also remove the mapply() S4 generic from
the BiocGenerics package. It's not needed anymore. base::mapply() should
work out-of-the-box on any object for which length() and [[ are
implemented.
H.
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
[[alternative HTML version deleted]]
_________________________________________________
Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
mailing list
https://stat.ethz.ch/mailman/__listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
