Re: [Bioc-devel] seq*apply deprecation
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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Program in Computational Biology
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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
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Re: [Bioc-devel] seq*apply deprecation
On Wed, Jan 22, 2014 at 1:29 PM, Hervé Pagès 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 +
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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--
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
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Re: [Bioc-devel] seq*apply deprecation
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 +
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
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Re: [Bioc-devel] seq*apply deprecation
Sounds good. But who is she?
On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès hpa...@fhcrc.org wrote:
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 +
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
[[alternative HTML version deleted]]
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Re: [Bioc-devel] seq*apply deprecation
On 01/22/2014 08:15 PM, Michael Lawrence wrote:
Sounds good. But who is she?
we would, she should, she would, we should... that's it! we should...
that's what I meant :-b
H.
On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
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
mailto: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 42139699d91a34c401eedd36db6271__6a607d0b06
Author: maechler maechler@00db46b3-68df-0310-__9c12-caf00c1e9a41
Date: Wed Nov 28 10:31:42 2012 +
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]]
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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
mailto:hpa...@fhcrc.org mailto:hpa...@fhcrc.org
Phone: (206) 667-5791 tel:%28206%29%20667-5791
tel:%28206%29%20667-5791
Fax: (206) 667-1319 tel:%28206%29%20667-1319
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 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
