Entering edit mode
Do we have a matrix-like object, but where the columns are Rle's?
Kasper
0
Entering edit mode
Patrick and I had talked about this a long time ago (essentially
putting a
"dim" attribute on an Rle), but the closest thing today is a DataFrame
with
Rle columns.
Use case?
Michael
On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:
> Do we have a matrix-like object, but where the columns are Rle's?
>
> Kasper
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
0
Entering edit mode
On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
<lawrence.michael at="" gene.com=""> wrote:
> Patrick and I had talked about this a long time ago (essentially
putting a
> "dim" attribute on an Rle), but the closest thing today is a
DataFrame with
> Rle columns.
>
> Use case?
Say I have whole-genome data (for example coverage) on multiple
samples. Usually, this is far easier to think of as a matrix (in my
opinion) with ~3B rows and I often want to do rowSums(), colSums() etc
(in fact, probably the whole API from matrixStats). This is
especially nice when you have multiple coverage-like tracks on each
sample, so you could have
trackA : genome by samples
trackB : genome by samples
...
You could think of this as a SummarizedExperiment, but with
_extremely_ big matrices in the assay slot.
I want to take advantage of the Rle structure to store the data more
efficiently and also to do potentially faster computations.
This is actually closer to my use case where I currently use matrices
with ~30M rows (which works fine), but I would like to expand to ~800M
rows (which would suck a bit).
You could also think of a matrix-like object with Rle columns as an
alternative sparse matrix structure. In a typical sparse matrix you
only store the non-zero entities, here we only store the
change-points. Depending on the structure of the matrix this could be
an efficient storage of an otherwise dense matrix.
So essentially, what I want, is to have mathematical operations on
this object, where I would utilize that I know that all entities are
numbers so the typical matrix operations makes sense.
[ side question which could be relevant in this discussion: for a
numeric Rle is there some notion of precision - say I have truly
numeric values with tons of digits, and I want to consider two numbers
part of the same run if |x1 -x2|<epsilon? ]="" kasper="">
> Michael
>
> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
> <kasperdanielhansen at="" gmail.com=""> wrote:
>>
>> Do we have a matrix-like object, but where the columns are Rle's?
>>
>> Kasper
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
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• link
12.5 years ago
Kasper Daniel Hansen
★
6.5k
0
Entering edit mode
On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
<kasperdanielhansen at="" gmail.com=""> wrote:
> On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
> <lawrence.michael at="" gene.com=""> wrote:
>> Patrick and I had talked about this a long time ago (essentially
putting a
>> "dim" attribute on an Rle), but the closest thing today is a
DataFrame with
>> Rle columns.
>>
>> Use case?
>
> Say I have whole-genome data (for example coverage) ?on multiple
> samples. ?Usually, this is far easier to think of as a matrix (in my
> opinion) with ~3B rows and I often want to do rowSums(), colSums()
etc
> (in fact, probably the whole API from matrixStats). ?This is
> especially nice when you have multiple coverage-like tracks on each
> sample, so you could have
> ?trackA : genome by samples
> ?trackB : genome by samples
> ?...
>
> You could think of this as a SummarizedExperiment, but with
> _extremely_ big matrices in the assay slot.
>
> I want to take advantage of the Rle structure to store the data more
> efficiently and also to do potentially faster computations.
>
> This is actually closer to my use case where I currently use
matrices
> with ~30M rows (which works fine), but I would like to expand to
~800M
> rows (which would suck a bit).
>
> You could also think of a matrix-like object with Rle columns as an
> alternative sparse matrix structure. ?In a typical sparse matrix you
> only store the non-zero entities, here we only store the
> change-points. ?Depending on the structure of the matrix this could
be
> an efficient storage of an otherwise dense matrix.
>
> So essentially, what I want, is to have mathematical operations on
> this object, where I would utilize that I know that all entities are
> numbers so the typical matrix operations makes sense.
>
> [ side question which could be relevant in this discussion: for a
> numeric Rle is there some notion of precision - say I have truly
> numeric values with tons of digits, and I want to consider two
numbers
> part of the same run if |x1 -x2|<epsilon? ]="" you="" can="" see="" that="" pete="" has="" had="" similar="" thoughts="" in="" genoset="" r="" dataframe-methods.r,="" although="" he="" only="" has="" colmeans="" (which="" is="" the="" easy="" one).="" kasper=""> Kasper
>
>>
>> Michael
>>
>> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>
>>> Do we have a matrix-like object, but where the columns are Rle's?
>>>
>>> Kasper
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
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• link
12.5 years ago
Kasper Daniel Hansen
★
6.5k
0
Entering edit mode
Seems like it could be a nice thing to have. Presumably one would
create an
Array subclass of Vector that would add a "dim" attribute. Then Matrix
could extend that to constrain dim to length two (unfortunately
colliding
with the Matrix class in the Matrix package). Then RleMatrix extends
Matrix
to implement the actual data storage and many of the accelerated
methods.
As you said, row-oriented methods would be tough.
Any takers?
Michael
On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:
> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
> <kasperdanielhansen@gmail.com> wrote:
> > On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
> > <lawrence.michael@gene.com> wrote:
> >> Patrick and I had talked about this a long time ago (essentially
> putting a
> >> "dim" attribute on an Rle), but the closest thing today is a
DataFrame
> with
> >> Rle columns.
> >>
> >> Use case?
> >
> > Say I have whole-genome data (for example coverage) on multiple
> > samples. Usually, this is far easier to think of as a matrix (in
my
> > opinion) with ~3B rows and I often want to do rowSums(), colSums()
etc
> > (in fact, probably the whole API from matrixStats). This is
> > especially nice when you have multiple coverage-like tracks on
each
> > sample, so you could have
> > trackA : genome by samples
> > trackB : genome by samples
> > ...
> >
> > You could think of this as a SummarizedExperiment, but with
> > _extremely_ big matrices in the assay slot.
> >
> > I want to take advantage of the Rle structure to store the data
more
> > efficiently and also to do potentially faster computations.
> >
> > This is actually closer to my use case where I currently use
matrices
> > with ~30M rows (which works fine), but I would like to expand to
~800M
> > rows (which would suck a bit).
> >
> > You could also think of a matrix-like object with Rle columns as
an
> > alternative sparse matrix structure. In a typical sparse matrix
you
> > only store the non-zero entities, here we only store the
> > change-points. Depending on the structure of the matrix this
could be
> > an efficient storage of an otherwise dense matrix.
> >
> > So essentially, what I want, is to have mathematical operations on
> > this object, where I would utilize that I know that all entities
are
> > numbers so the typical matrix operations makes sense.
> >
> > [ side question which could be relevant in this discussion: for a
> > numeric Rle is there some notion of precision - say I have truly
> > numeric values with tons of digits, and I want to consider two
numbers
> > part of the same run if |x1 -x2|<epsilon? ]="">
> You can see that Pete has had similar thoughts in
> genoset/R/DataFrame-methods.R, although he only has colMeans (which
is
> the easy one).
>
> Kasper
>
> > Kasper
> >
> >>
> >> Michael
> >>
> >> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
> >> <kasperdanielhansen@gmail.com> wrote:
> >>>
> >>> Do we have a matrix-like object, but where the columns are
Rle's?
> >>>
> >>> Kasper
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
>
[[alternative HTML version deleted]]
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• link
12.5 years ago
Michael Lawrence
★
11k
0
Entering edit mode
One comment: since matrix is a vector with a dim attribute I see that
the natural parallel is doing the same for Rle. Nevertheless, that
would put an upper limit on the number of runLengths in the entire
matrix. My impression (which could be wrong) is that we would need to
implement essentially all matrix-like numeric operations from scratch
anyway, so it may be worthwhile to consider using a list of Rle's
where each Rle is a column, instead of a single Rle to represent all
columns. Clearly that depends on implementation details, but if we
really need to do everything from scratch, a list of columns might be
more flexible (and perhaps even easier to code).
Kasper
On Tue, Jun 26, 2012 at 6:41 AM, Michael Lawrence
<lawrence.michael at="" gene.com=""> wrote:
> Seems like it could be a nice thing to have. Presumably one would
create an
> Array subclass of Vector that would add a "dim" attribute. Then
Matrix could
> extend that to constrain dim to length two (unfortunately colliding
with the
> Matrix class in the Matrix package). Then RleMatrix extends Matrix
to
> implement the actual data storage and many of the accelerated
methods. As
> you said, row-oriented methods would be tough.
>
> Any takers?
>
> Michael
>
> On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen
> <kasperdanielhansen at="" gmail.com=""> wrote:
>>
>> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at="" gmail.com=""> wrote:
>> > On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
>> > <lawrence.michael at="" gene.com=""> wrote:
>> >> Patrick and I had talked about this a long time ago (essentially
>> >> putting a
>> >> "dim" attribute on an Rle), but the closest thing today is a
DataFrame
>> >> with
>> >> Rle columns.
>> >>
>> >> Use case?
>> >
>> > Say I have whole-genome data (for example coverage) ?on multiple
>> > samples. ?Usually, this is far easier to think of as a matrix (in
my
>> > opinion) with ~3B rows and I often want to do rowSums(),
colSums() etc
>> > (in fact, probably the whole API from matrixStats). ?This is
>> > especially nice when you have multiple coverage-like tracks on
each
>> > sample, so you could have
>> > ?trackA : genome by samples
>> > ?trackB : genome by samples
>> > ?...
>> >
>> > You could think of this as a SummarizedExperiment, but with
>> > _extremely_ big matrices in the assay slot.
>> >
>> > I want to take advantage of the Rle structure to store the data
more
>> > efficiently and also to do potentially faster computations.
>> >
>> > This is actually closer to my use case where I currently use
matrices
>> > with ~30M rows (which works fine), but I would like to expand to
~800M
>> > rows (which would suck a bit).
>> >
>> > You could also think of a matrix-like object with Rle columns as
an
>> > alternative sparse matrix structure. ?In a typical sparse matrix
you
>> > only store the non-zero entities, here we only store the
>> > change-points. ?Depending on the structure of the matrix this
could be
>> > an efficient storage of an otherwise dense matrix.
>> >
>> > So essentially, what I want, is to have mathematical operations
on
>> > this object, where I would utilize that I know that all entities
are
>> > numbers so the typical matrix operations makes sense.
>> >
>> > [ side question which could be relevant in this discussion: for a
>> > numeric Rle is there some notion of precision - say I have truly
>> > numeric values with tons of digits, and I want to consider two
numbers
>> > part of the same run if |x1 -x2|<epsilon? ]="">>
>> You can see that Pete has had similar thoughts in
>> genoset/R/DataFrame-methods.R, although he only has colMeans (which
is
>> the easy one).
>>
>> Kasper
>>
>> > Kasper
>> >
>> >>
>> >> Michael
>> >>
>> >> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>> >> <kasperdanielhansen at="" gmail.com=""> wrote:
>> >>>
>> >>> Do we have a matrix-like object, but where the columns are
Rle's?
>> >>>
>> >>> Kasper
>> >>>
>> >>> _______________________________________________
>> >>> Bioconductor mailing list
>> >>> Bioconductor at r-project.org
>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >>> Search the archives:
>> >>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >>
>> >>
>
>
ADD REPLY
• link
12.5 years ago
Kasper Daniel Hansen
★
6.5k
0
Entering edit mode
On Wed, Jun 27, 2012 at 8:07 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:
> One comment: since matrix is a vector with a dim attribute I see
that
> the natural parallel is doing the same for Rle.
Right, in the original plan, the Array class would bring the dim
attribute,
and RleMatrix would contain both Matrix and Rle.
> Nevertheless, that
> would put an upper limit on the number of runLengths in the entire
> matrix. My impression (which could be wrong) is that we would need
to
> implement essentially all matrix-like numeric operations from
scratch
> anyway, so it may be worthwhile to consider using a list of Rle's
> where each Rle is a column, instead of a single Rle to represent all
> columns. Clearly that depends on implementation details, but if we
> really need to do everything from scratch, a list of columns might
be
> more flexible (and perhaps even easier to code).
>
>
This would make it harder to treat RleMatrix as an Rle (which is a
nice
feature of base R matrices). If the problem is the vector length
limit,
then I'd rather wait for Luke's fix, which apparently is coming along.
Kasper
>
> On Tue, Jun 26, 2012 at 6:41 AM, Michael Lawrence
> <lawrence.michael@gene.com> wrote:
> > Seems like it could be a nice thing to have. Presumably one would
create
> an
> > Array subclass of Vector that would add a "dim" attribute. Then
Matrix
> could
> > extend that to constrain dim to length two (unfortunately
colliding with
> the
> > Matrix class in the Matrix package). Then RleMatrix extends Matrix
to
> > implement the actual data storage and many of the accelerated
methods. As
> > you said, row-oriented methods would be tough.
> >
> > Any takers?
> >
> > Michael
> >
> > On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen
> > <kasperdanielhansen@gmail.com> wrote:
> >>
> >> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
> >> <kasperdanielhansen@gmail.com> wrote:
> >> > On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
> >> > <lawrence.michael@gene.com> wrote:
> >> >> Patrick and I had talked about this a long time ago
(essentially
> >> >> putting a
> >> >> "dim" attribute on an Rle), but the closest thing today is a
> DataFrame
> >> >> with
> >> >> Rle columns.
> >> >>
> >> >> Use case?
> >> >
> >> > Say I have whole-genome data (for example coverage) on
multiple
> >> > samples. Usually, this is far easier to think of as a matrix
(in my
> >> > opinion) with ~3B rows and I often want to do rowSums(),
colSums() etc
> >> > (in fact, probably the whole API from matrixStats). This is
> >> > especially nice when you have multiple coverage-like tracks on
each
> >> > sample, so you could have
> >> > trackA : genome by samples
> >> > trackB : genome by samples
> >> > ...
> >> >
> >> > You could think of this as a SummarizedExperiment, but with
> >> > _extremely_ big matrices in the assay slot.
> >> >
> >> > I want to take advantage of the Rle structure to store the data
more
> >> > efficiently and also to do potentially faster computations.
> >> >
> >> > This is actually closer to my use case where I currently use
matrices
> >> > with ~30M rows (which works fine), but I would like to expand
to ~800M
> >> > rows (which would suck a bit).
> >> >
> >> > You could also think of a matrix-like object with Rle columns
as an
> >> > alternative sparse matrix structure. In a typical sparse
matrix you
> >> > only store the non-zero entities, here we only store the
> >> > change-points. Depending on the structure of the matrix this
could be
> >> > an efficient storage of an otherwise dense matrix.
> >> >
> >> > So essentially, what I want, is to have mathematical operations
on
> >> > this object, where I would utilize that I know that all
entities are
> >> > numbers so the typical matrix operations makes sense.
> >> >
> >> > [ side question which could be relevant in this discussion: for
a
> >> > numeric Rle is there some notion of precision - say I have
truly
> >> > numeric values with tons of digits, and I want to consider two
numbers
> >> > part of the same run if |x1 -x2|<epsilon? ]=""> >>
> >> You can see that Pete has had similar thoughts in
> >> genoset/R/DataFrame-methods.R, although he only has colMeans
(which is
> >> the easy one).
> >>
> >> Kasper
> >>
> >> > Kasper
> >> >
> >> >>
> >> >> Michael
> >> >>
> >> >> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
> >> >> <kasperdanielhansen@gmail.com> wrote:
> >> >>>
> >> >>> Do we have a matrix-like object, but where the columns are
Rle's?
> >> >>>
> >> >>> Kasper
> >> >>>
> >> >>> _______________________________________________
> >> >>> Bioconductor mailing list
> >> >>> Bioconductor@r-project.org
> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >>> Search the archives:
> >> >>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >>
> >> >>
> >
> >
>
[[alternative HTML version deleted]]
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• link
12.5 years ago
Michael Lawrence
★
11k
0
Entering edit mode
I would love/use all the time this feature if it existed.
Jeff
On Wed, Jun 27, 2012 at 11:21 AM, Michael Lawrence
<lawrence.michael at="" gene.com=""> wrote:
> On Wed, Jun 27, 2012 at 8:07 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> One comment: ?since matrix is a vector with a dim attribute I see
that
>> the natural parallel is doing the same for Rle.
>
>
> Right, in the original plan, the Array class would bring the dim
attribute,
> and RleMatrix would contain both Matrix and Rle.
>
>
>> ?Nevertheless, that
>> would put an upper limit on the number of runLengths in the entire
>> matrix. ?My impression (which could be wrong) is that we would need
to
>> implement essentially all matrix-like numeric operations from
scratch
>> anyway, so it may be worthwhile to consider using a list of Rle's
>> where each Rle is a column, instead of a single Rle to represent
all
>> columns. ?Clearly that depends on implementation details, but if we
>> really need to do everything from scratch, a list of columns might
be
>> more flexible (and perhaps even easier to code).
>>
>>
> This would make it harder to treat RleMatrix as an Rle (which is a
nice
> feature of base R matrices). If the problem is the vector length
limit,
> then I'd rather wait for Luke's fix, which apparently is coming
along.
>
> Kasper
>>
>> On Tue, Jun 26, 2012 at 6:41 AM, Michael Lawrence
>> <lawrence.michael at="" gene.com=""> wrote:
>> > Seems like it could be a nice thing to have. Presumably one would
create
>> an
>> > Array subclass of Vector that would add a "dim" attribute. Then
Matrix
>> could
>> > extend that to constrain dim to length two (unfortunately
colliding with
>> the
>> > Matrix class in the Matrix package). Then RleMatrix extends
Matrix to
>> > implement the actual data storage and many of the accelerated
methods. As
>> > you said, row-oriented methods would be tough.
>> >
>> > Any takers?
>> >
>> > Michael
>> >
>> > On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen
>> > <kasperdanielhansen at="" gmail.com=""> wrote:
>> >>
>> >> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
>> >> <kasperdanielhansen at="" gmail.com=""> wrote:
>> >> > On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
>> >> > <lawrence.michael at="" gene.com=""> wrote:
>> >> >> Patrick and I had talked about this a long time ago
(essentially
>> >> >> putting a
>> >> >> "dim" attribute on an Rle), but the closest thing today is a
>> DataFrame
>> >> >> with
>> >> >> Rle columns.
>> >> >>
>> >> >> Use case?
>> >> >
>> >> > Say I have whole-genome data (for example coverage) ?on
multiple
>> >> > samples. ?Usually, this is far easier to think of as a matrix
(in my
>> >> > opinion) with ~3B rows and I often want to do rowSums(),
colSums() etc
>> >> > (in fact, probably the whole API from matrixStats). ?This is
>> >> > especially nice when you have multiple coverage-like tracks on
each
>> >> > sample, so you could have
>> >> > ?trackA : genome by samples
>> >> > ?trackB : genome by samples
>> >> > ?...
>> >> >
>> >> > You could think of this as a SummarizedExperiment, but with
>> >> > _extremely_ big matrices in the assay slot.
>> >> >
>> >> > I want to take advantage of the Rle structure to store the
data more
>> >> > efficiently and also to do potentially faster computations.
>> >> >
>> >> > This is actually closer to my use case where I currently use
matrices
>> >> > with ~30M rows (which works fine), but I would like to expand
to ~800M
>> >> > rows (which would suck a bit).
>> >> >
>> >> > You could also think of a matrix-like object with Rle columns
as an
>> >> > alternative sparse matrix structure. ?In a typical sparse
matrix you
>> >> > only store the non-zero entities, here we only store the
>> >> > change-points. ?Depending on the structure of the matrix this
could be
>> >> > an efficient storage of an otherwise dense matrix.
>> >> >
>> >> > So essentially, what I want, is to have mathematical
operations on
>> >> > this object, where I would utilize that I know that all
entities are
>> >> > numbers so the typical matrix operations makes sense.
>> >> >
>> >> > [ side question which could be relevant in this discussion:
for a
>> >> > numeric Rle is there some notion of precision - say I have
truly
>> >> > numeric values with tons of digits, and I want to consider two
numbers
>> >> > part of the same run if |x1 -x2|<epsilon? ]="">> >>
>> >> You can see that Pete has had similar thoughts in
>> >> genoset/R/DataFrame-methods.R, although he only has colMeans
(which is
>> >> the easy one).
>> >>
>> >> Kasper
>> >>
>> >> > Kasper
>> >> >
>> >> >>
>> >> >> Michael
>> >> >>
>> >> >> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>> >> >> <kasperdanielhansen at="" gmail.com=""> wrote:
>> >> >>>
>> >> >>> Do we have a matrix-like object, but where the columns are
Rle's?
>> >> >>>
>> >> >>> Kasper
>> >> >>>
>> >> >>> _______________________________________________
>> >> >>> Bioconductor mailing list
>> >> >>> Bioconductor at r-project.org
>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> >>> Search the archives:
>> >> >>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >> >>
>> >> >>
>> >
>> >
>>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
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• link
12.5 years ago
Jeff Leek
▴
650
0
Entering edit mode
Hi guys,
Note that some of the things in the "matrix API" seem to work on
standard data frames:
> df <- data.frame(aa=1:5, bb=100)
> rowSums(df)
[1] 101 102 103 104 105
> colSums(df)
aa bb
15 500
> max(df)
[1] 100
> min(df)
[1] 1
> range(df)
[1] 1 100
> df + df
aa bb
1 2 200
2 4 200
3 6 200
4 8 200
5 10 200
> df <= 3
aa bb
[1,] TRUE FALSE
[2,] TRUE FALSE
[3,] TRUE FALSE
[4,] FALSE FALSE
[5,] FALSE FALSE
etc...
But none of them work on DataFrame. Maybe if they were we wouldn't
need
RleMatrix? Using DataFrame instead of RleMatrix would be nice because
it
reuses what we already have. It would also avoid the pitfall of having
the length of an RleMatrix not being representable with a 32-bit int
when let's say the nb of rows is 800M and there are a few nb of cols
(like in Kasper's use case). No need to wait for Luke's "big vector"
hack.
Cheers,
H.
On 06/27/2012 10:46 AM, Jeff Leek wrote:
> I would love/use all the time this feature if it existed.
>
> Jeff
>
> On Wed, Jun 27, 2012 at 11:21 AM, Michael Lawrence
> <lawrence.michael at="" gene.com=""> wrote:
>> On Wed, Jun 27, 2012 at 8:07 AM, Kasper Daniel Hansen <
>> kasperdanielhansen at gmail.com> wrote:
>>
>>> One comment: since matrix is a vector with a dim attribute I see
that
>>> the natural parallel is doing the same for Rle.
>>
>>
>> Right, in the original plan, the Array class would bring the dim
attribute,
>> and RleMatrix would contain both Matrix and Rle.
>>
>>
>>> Nevertheless, that
>>> would put an upper limit on the number of runLengths in the entire
>>> matrix. My impression (which could be wrong) is that we would
need to
>>> implement essentially all matrix-like numeric operations from
scratch
>>> anyway, so it may be worthwhile to consider using a list of Rle's
>>> where each Rle is a column, instead of a single Rle to represent
all
>>> columns. Clearly that depends on implementation details, but if
we
>>> really need to do everything from scratch, a list of columns might
be
>>> more flexible (and perhaps even easier to code).
>>>
>>>
>> This would make it harder to treat RleMatrix as an Rle (which is a
nice
>> feature of base R matrices). If the problem is the vector length
limit,
>> then I'd rather wait for Luke's fix, which apparently is coming
along.
>>
>> Kasper
>>>
>>> On Tue, Jun 26, 2012 at 6:41 AM, Michael Lawrence
>>> <lawrence.michael at="" gene.com=""> wrote:
>>>> Seems like it could be a nice thing to have. Presumably one would
create
>>> an
>>>> Array subclass of Vector that would add a "dim" attribute. Then
Matrix
>>> could
>>>> extend that to constrain dim to length two (unfortunately
colliding with
>>> the
>>>> Matrix class in the Matrix package). Then RleMatrix extends
Matrix to
>>>> implement the actual data storage and many of the accelerated
methods. As
>>>> you said, row-oriented methods would be tough.
>>>>
>>>> Any takers?
>>>>
>>>> Michael
>>>>
>>>> On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen
>>>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>>>
>>>>> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
>>>>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>>>> On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
>>>>>> <lawrence.michael at="" gene.com=""> wrote:
>>>>>>> Patrick and I had talked about this a long time ago
(essentially
>>>>>>> putting a
>>>>>>> "dim" attribute on an Rle), but the closest thing today is a
>>> DataFrame
>>>>>>> with
>>>>>>> Rle columns.
>>>>>>>
>>>>>>> Use case?
>>>>>>
>>>>>> Say I have whole-genome data (for example coverage) on
multiple
>>>>>> samples. Usually, this is far easier to think of as a matrix
(in my
>>>>>> opinion) with ~3B rows and I often want to do rowSums(),
colSums() etc
>>>>>> (in fact, probably the whole API from matrixStats). This is
>>>>>> especially nice when you have multiple coverage-like tracks on
each
>>>>>> sample, so you could have
>>>>>> trackA : genome by samples
>>>>>> trackB : genome by samples
>>>>>> ...
>>>>>>
>>>>>> You could think of this as a SummarizedExperiment, but with
>>>>>> _extremely_ big matrices in the assay slot.
>>>>>>
>>>>>> I want to take advantage of the Rle structure to store the data
more
>>>>>> efficiently and also to do potentially faster computations.
>>>>>>
>>>>>> This is actually closer to my use case where I currently use
matrices
>>>>>> with ~30M rows (which works fine), but I would like to expand
to ~800M
>>>>>> rows (which would suck a bit).
>>>>>>
>>>>>> You could also think of a matrix-like object with Rle columns
as an
>>>>>> alternative sparse matrix structure. In a typical sparse
matrix you
>>>>>> only store the non-zero entities, here we only store the
>>>>>> change-points. Depending on the structure of the matrix this
could be
>>>>>> an efficient storage of an otherwise dense matrix.
>>>>>>
>>>>>> So essentially, what I want, is to have mathematical operations
on
>>>>>> this object, where I would utilize that I know that all
entities are
>>>>>> numbers so the typical matrix operations makes sense.
>>>>>>
>>>>>> [ side question which could be relevant in this discussion: for
a
>>>>>> numeric Rle is there some notion of precision - say I have
truly
>>>>>> numeric values with tons of digits, and I want to consider two
numbers
>>>>>> part of the same run if |x1 -x2|<epsilon? ]="">>>>>
>>>>> You can see that Pete has had similar thoughts in
>>>>> genoset/R/DataFrame-methods.R, although he only has colMeans
(which is
>>>>> the easy one).
>>>>>
>>>>> Kasper
>>>>>
>>>>>> Kasper
>>>>>>
>>>>>>>
>>>>>>> Michael
>>>>>>>
>>>>>>> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>>>>>>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>>>>>>
>>>>>>>> Do we have a matrix-like object, but where the columns are
Rle's?
>>>>>>>>
>>>>>>>> Kasper
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioconductor mailing list
>>>>>>>> Bioconductor at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>> Search the archives:
>>>>>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>
>>>>>>>
>>>>
>>>>
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
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: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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• link
12.5 years ago
Hervé Pagès
16k
0
Entering edit mode
On Wed, Jun 27, 2012 at 3:30 PM, Hervé Pagès <hpages at="" fhcrc.org="">
wrote:
> Hi guys,
>
> Note that some of the things in the "matrix API" seem to work on
> standard data frames:
>
>> df <- data.frame(aa=1:5, bb=100)
>> rowSums(df)
> [1] 101 102 103 104 105
>> colSums(df)
> ?aa ?bb
> ?15 500
>> max(df)
> [1] 100
>> min(df)
> [1] 1
>> range(df)
> [1] ? 1 100
>> df + df
> ?aa ?bb
> 1 ?2 200
> 2 ?4 200
> 3 ?6 200
> 4 ?8 200
> 5 10 200
>> df <= 3
> ? ? ? ?aa ? ?bb
> [1,] ?TRUE FALSE
> [2,] ?TRUE FALSE
> [3,] ?TRUE FALSE
> [4,] FALSE FALSE
> [5,] FALSE FALSE
>
> etc...
>
> But none of them work on DataFrame. Maybe if they were we wouldn't
need
> RleMatrix? Using DataFrame instead of RleMatrix would be nice
because it
> reuses what we already have. It would also avoid the pitfall of
having
> the length of an RleMatrix not being representable with a 32-bit int
> when let's say the nb of rows is 800M and there are a few nb of cols
> (like in Kasper's use case). No need to wait for Luke's "big vector"
> hack.
This is totally fine with me, as long as coercion from Rle to a normal
vector is avoided.
But it might make sense to have a derivative class ensuring that all
columns are numeric in nature.
Kasper
>
> Cheers,
> H.
>
>
> On 06/27/2012 10:46 AM, Jeff Leek wrote:
>>
>> I would love/use all the time this feature if it existed.
>>
>> Jeff
>>
>> On Wed, Jun 27, 2012 at 11:21 AM, Michael Lawrence
>> <lawrence.michael at="" gene.com=""> wrote:
>>>
>>> On Wed, Jun 27, 2012 at 8:07 AM, Kasper Daniel Hansen <
>>> kasperdanielhansen at gmail.com> wrote:
>>>
>>>> One comment: ?since matrix is a vector with a dim attribute I see
that
>>>> the natural parallel is doing the same for Rle.
>>>
>>>
>>>
>>> Right, in the original plan, the Array class would bring the dim
>>> attribute,
>>> and RleMatrix would contain both Matrix and Rle.
>>>
>>>
>>>> ?Nevertheless, that
>>>> would put an upper limit on the number of runLengths in the
entire
>>>> matrix. ?My impression (which could be wrong) is that we would
need to
>>>> implement essentially all matrix-like numeric operations from
scratch
>>>> anyway, so it may be worthwhile to consider using a list of Rle's
>>>> where each Rle is a column, instead of a single Rle to represent
all
>>>> columns. ?Clearly that depends on implementation details, but if
we
>>>> really need to do everything from scratch, a list of columns
might be
>>>> more flexible (and perhaps even easier to code).
>>>>
>>>>
>>> This would make it harder to treat RleMatrix as an Rle (which is a
nice
>>> feature of base R matrices). If the problem is the vector length
limit,
>>> then I'd rather wait for Luke's fix, which apparently is coming
along.
>>>
>>> Kasper
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 6:41 AM, Michael Lawrence
>>>> <lawrence.michael at="" gene.com=""> wrote:
>>>>>
>>>>> Seems like it could be a nice thing to have. Presumably one
would
>>>>> create
>>>>
>>>> an
>>>>>
>>>>> Array subclass of Vector that would add a "dim" attribute. Then
Matrix
>>>>
>>>> could
>>>>>
>>>>> extend that to constrain dim to length two (unfortunately
colliding
>>>>> with
>>>>
>>>> the
>>>>>
>>>>> Matrix class in the Matrix package). Then RleMatrix extends
Matrix to
>>>>> implement the actual data storage and many of the accelerated
methods.
>>>>> As
>>>>> you said, row-oriented methods would be tough.
>>>>>
>>>>> Any takers?
>>>>>
>>>>> Michael
>>>>>
>>>>> On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen
>>>>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>>>>
>>>>>>
>>>>>> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
>>>>>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>>>>>
>>>>>>> On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
>>>>>>> <lawrence.michael at="" gene.com=""> wrote:
>>>>>>>>
>>>>>>>> Patrick and I had talked about this a long time ago
(essentially
>>>>>>>> putting a
>>>>>>>> "dim" attribute on an Rle), but the closest thing today is a
>>>>
>>>> DataFrame
>>>>>>>>
>>>>>>>> with
>>>>>>>> Rle columns.
>>>>>>>>
>>>>>>>> Use case?
>>>>>>>
>>>>>>>
>>>>>>> Say I have whole-genome data (for example coverage) ?on
multiple
>>>>>>> samples. ?Usually, this is far easier to think of as a matrix
(in my
>>>>>>> opinion) with ~3B rows and I often want to do rowSums(),
colSums()
>>>>>>> etc
>>>>>>> (in fact, probably the whole API from matrixStats). ?This is
>>>>>>> especially nice when you have multiple coverage-like tracks on
each
>>>>>>> sample, so you could have
>>>>>>> ?trackA : genome by samples
>>>>>>> ?trackB : genome by samples
>>>>>>> ?...
>>>>>>>
>>>>>>> You could think of this as a SummarizedExperiment, but with
>>>>>>> _extremely_ big matrices in the assay slot.
>>>>>>>
>>>>>>> I want to take advantage of the Rle structure to store the
data more
>>>>>>> efficiently and also to do potentially faster computations.
>>>>>>>
>>>>>>> This is actually closer to my use case where I currently use
matrices
>>>>>>> with ~30M rows (which works fine), but I would like to expand
to
>>>>>>> ~800M
>>>>>>> rows (which would suck a bit).
>>>>>>>
>>>>>>> You could also think of a matrix-like object with Rle columns
as an
>>>>>>> alternative sparse matrix structure. ?In a typical sparse
matrix you
>>>>>>> only store the non-zero entities, here we only store the
>>>>>>> change-points. ?Depending on the structure of the matrix this
could
>>>>>>> be
>>>>>>> an efficient storage of an otherwise dense matrix.
>>>>>>>
>>>>>>> So essentially, what I want, is to have mathematical
operations on
>>>>>>> this object, where I would utilize that I know that all
entities are
>>>>>>> numbers so the typical matrix operations makes sense.
>>>>>>>
>>>>>>> [ side question which could be relevant in this discussion:
for a
>>>>>>> numeric Rle is there some notion of precision - say I have
truly
>>>>>>> numeric values with tons of digits, and I want to consider two
>>>>>>> numbers
>>>>>>> part of the same run if |x1 -x2|<epsilon? ]="">>>>>>
>>>>>>
>>>>>> You can see that Pete has had similar thoughts in
>>>>>> genoset/R/DataFrame-methods.R, although he only has colMeans
(which is
>>>>>> the easy one).
>>>>>>
>>>>>> Kasper
>>>>>>
>>>>>>> Kasper
>>>>>>>
>>>>>>>>
>>>>>>>> Michael
>>>>>>>>
>>>>>>>> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>>>>>>>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Do we have a matrix-like object, but where the columns are
Rle's?
>>>>>>>>>
>>>>>>>>> Kasper
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioconductor mailing list
>>>>>>>>> Bioconductor at r-project.org
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>>> Search the archives:
>>>>>>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>> ? ? ? ?[[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
> --
> 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: hpages at fhcrc.org
> Phone: ?(206) 667-5791
> Fax: ? ?(206) 667-1319
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY
• link
12.5 years ago
Kasper Daniel Hansen
★
6.5k
0
Entering edit mode
It does seem that the R data.frame tries its best to act like a
matrix. For
example, df + 1 and paste(df, "foo") act as one would expect. I've
never
used it in this way, probably because it's best to use matrices for
that
sort of thing
Kasper, maybe you could list out the types of operations you would
require?
For example, colSums, rowSums, ....
In terms of performance, is the number of columns small enough for
iteration in R? We could fast-path the special case where every column
is
an Rle, but in general it would be hard to push that down into C.
Michael
On Wed, Jun 27, 2012 at 12:54 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:
> On Wed, Jun 27, 2012 at 3:30 PM, Hervé Pagès <hpages@fhcrc.org>
wrote:
> > Hi guys,
> >
> > Note that some of the things in the "matrix API" seem to work on
> > standard data frames:
> >
> >> df <- data.frame(aa=1:5, bb=100)
> >> rowSums(df)
> > [1] 101 102 103 104 105
> >> colSums(df)
> > aa bb
> > 15 500
> >> max(df)
> > [1] 100
> >> min(df)
> > [1] 1
> >> range(df)
> > [1] 1 100
> >> df + df
> > aa bb
> > 1 2 200
> > 2 4 200
> > 3 6 200
> > 4 8 200
> > 5 10 200
> >> df <= 3
> > aa bb
> > [1,] TRUE FALSE
> > [2,] TRUE FALSE
> > [3,] TRUE FALSE
> > [4,] FALSE FALSE
> > [5,] FALSE FALSE
> >
> > etc...
> >
> > But none of them work on DataFrame. Maybe if they were we wouldn't
need
> > RleMatrix? Using DataFrame instead of RleMatrix would be nice
because it
> > reuses what we already have. It would also avoid the pitfall of
having
> > the length of an RleMatrix not being representable with a 32-bit
int
> > when let's say the nb of rows is 800M and there are a few nb of
cols
> > (like in Kasper's use case). No need to wait for Luke's "big
vector"
> > hack.
>
> This is totally fine with me, as long as coercion from Rle to a
normal
> vector is avoided.
>
> But it might make sense to have a derivative class ensuring that all
> columns are numeric in nature.
>
> Kasper
>
> >
> > Cheers,
> > H.
> >
> >
> > On 06/27/2012 10:46 AM, Jeff Leek wrote:
> >>
> >> I would love/use all the time this feature if it existed.
> >>
> >> Jeff
> >>
> >> On Wed, Jun 27, 2012 at 11:21 AM, Michael Lawrence
> >> <lawrence.michael@gene.com> wrote:
> >>>
> >>> On Wed, Jun 27, 2012 at 8:07 AM, Kasper Daniel Hansen <
> >>> kasperdanielhansen@gmail.com> wrote:
> >>>
> >>>> One comment: since matrix is a vector with a dim attribute I
see that
> >>>> the natural parallel is doing the same for Rle.
> >>>
> >>>
> >>>
> >>> Right, in the original plan, the Array class would bring the dim
> >>> attribute,
> >>> and RleMatrix would contain both Matrix and Rle.
> >>>
> >>>
> >>>> Nevertheless, that
> >>>> would put an upper limit on the number of runLengths in the
entire
> >>>> matrix. My impression (which could be wrong) is that we would
need to
> >>>> implement essentially all matrix-like numeric operations from
scratch
> >>>> anyway, so it may be worthwhile to consider using a list of
Rle's
> >>>> where each Rle is a column, instead of a single Rle to
represent all
> >>>> columns. Clearly that depends on implementation details, but
if we
> >>>> really need to do everything from scratch, a list of columns
might be
> >>>> more flexible (and perhaps even easier to code).
> >>>>
> >>>>
> >>> This would make it harder to treat RleMatrix as an Rle (which is
a nice
> >>> feature of base R matrices). If the problem is the vector length
limit,
> >>> then I'd rather wait for Luke's fix, which apparently is coming
along.
> >>>
> >>> Kasper
> >>>>
> >>>>
> >>>> On Tue, Jun 26, 2012 at 6:41 AM, Michael Lawrence
> >>>> <lawrence.michael@gene.com> wrote:
> >>>>>
> >>>>> Seems like it could be a nice thing to have. Presumably one
would
> >>>>> create
> >>>>
> >>>> an
> >>>>>
> >>>>> Array subclass of Vector that would add a "dim" attribute.
Then
> Matrix
> >>>>
> >>>> could
> >>>>>
> >>>>> extend that to constrain dim to length two (unfortunately
colliding
> >>>>> with
> >>>>
> >>>> the
> >>>>>
> >>>>> Matrix class in the Matrix package). Then RleMatrix extends
Matrix to
> >>>>> implement the actual data storage and many of the accelerated
> methods.
> >>>>> As
> >>>>> you said, row-oriented methods would be tough.
> >>>>>
> >>>>> Any takers?
> >>>>>
> >>>>> Michael
> >>>>>
> >>>>> On Mon, Jun 25, 2012 at 9:11 PM, Kasper Daniel Hansen
> >>>>> <kasperdanielhansen@gmail.com> wrote:
> >>>>>>
> >>>>>>
> >>>>>> On Mon, Jun 25, 2012 at 11:56 PM, Kasper Daniel Hansen
> >>>>>> <kasperdanielhansen@gmail.com> wrote:
> >>>>>>>
> >>>>>>> On Mon, Jun 25, 2012 at 11:36 PM, Michael Lawrence
> >>>>>>> <lawrence.michael@gene.com> wrote:
> >>>>>>>>
> >>>>>>>> Patrick and I had talked about this a long time ago
(essentially
> >>>>>>>> putting a
> >>>>>>>> "dim" attribute on an Rle), but the closest thing today is
a
> >>>>
> >>>> DataFrame
> >>>>>>>>
> >>>>>>>> with
> >>>>>>>> Rle columns.
> >>>>>>>>
> >>>>>>>> Use case?
> >>>>>>>
> >>>>>>>
> >>>>>>> Say I have whole-genome data (for example coverage) on
multiple
> >>>>>>> samples. Usually, this is far easier to think of as a
matrix (in
> my
> >>>>>>> opinion) with ~3B rows and I often want to do rowSums(),
colSums()
> >>>>>>> etc
> >>>>>>> (in fact, probably the whole API from matrixStats). This is
> >>>>>>> especially nice when you have multiple coverage-like tracks
on each
> >>>>>>> sample, so you could have
> >>>>>>> trackA : genome by samples
> >>>>>>> trackB : genome by samples
> >>>>>>> ...
> >>>>>>>
> >>>>>>> You could think of this as a SummarizedExperiment, but with
> >>>>>>> _extremely_ big matrices in the assay slot.
> >>>>>>>
> >>>>>>> I want to take advantage of the Rle structure to store the
data
> more
> >>>>>>> efficiently and also to do potentially faster computations.
> >>>>>>>
> >>>>>>> This is actually closer to my use case where I currently use
> matrices
> >>>>>>> with ~30M rows (which works fine), but I would like to
expand to
> >>>>>>> ~800M
> >>>>>>> rows (which would suck a bit).
> >>>>>>>
> >>>>>>> You could also think of a matrix-like object with Rle
columns as an
> >>>>>>> alternative sparse matrix structure. In a typical sparse
matrix
> you
> >>>>>>> only store the non-zero entities, here we only store the
> >>>>>>> change-points. Depending on the structure of the matrix
this could
> >>>>>>> be
> >>>>>>> an efficient storage of an otherwise dense matrix.
> >>>>>>>
> >>>>>>> So essentially, what I want, is to have mathematical
operations on
> >>>>>>> this object, where I would utilize that I know that all
entities
> are
> >>>>>>> numbers so the typical matrix operations makes sense.
> >>>>>>>
> >>>>>>> [ side question which could be relevant in this discussion:
for a
> >>>>>>> numeric Rle is there some notion of precision - say I have
truly
> >>>>>>> numeric values with tons of digits, and I want to consider
two
> >>>>>>> numbers
> >>>>>>> part of the same run if |x1 -x2|<epsilon? ]=""> >>>>>>
> >>>>>>
> >>>>>> You can see that Pete has had similar thoughts in
> >>>>>> genoset/R/DataFrame-methods.R, although he only has colMeans
(which
> is
> >>>>>> the easy one).
> >>>>>>
> >>>>>> Kasper
> >>>>>>
> >>>>>>> Kasper
> >>>>>>>
> >>>>>>>>
> >>>>>>>> Michael
> >>>>>>>>
> >>>>>>>> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
> >>>>>>>> <kasperdanielhansen@gmail.com> wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Do we have a matrix-like object, but where the columns are
Rle's?
> >>>>>>>>>
> >>>>>>>>> Kasper
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> Bioconductor mailing list
> >>>>>>>>> Bioconductor@r-project.org
> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>>>>>> Search the archives:
> >>>>>>>>>
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>
> >>>>>
> >>>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> > --
> > 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: hpages@fhcrc.org
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
ADD REPLY
• link
12.5 years ago
Michael Lawrence
★
11k
0
Entering edit mode
Hi Kasper,
On 06/25/2012 08:56 PM, Kasper Daniel Hansen wrote:
[...]
> [ side question which could be relevant in this discussion: for a
> numeric Rle is there some notion of precision - say I have truly
> numeric values with tons of digits, and I want to consider two
numbers
> part of the same run if |x1 -x2|<epsilon? ]="" the="" comparison="" of="" 2="" doubles="" is="" done="" at="" the="" c="" level="" with="=," which="" afaik="" is="" the="" same="" as="" doing="=" in="" r="" (as="" long="" as="" we="" deal="" with="" non-na="" and="" non-nan="" values).="" see="" the="" _fill_rle_slots_with_double_vals()="" helper="" function="" in="" iranges="" src="" rle_class.c="" for="" the="" details.="" therefore:=""> all.equal(sqrt(3)^2, 3)
[1] TRUE
> sqrt(3)^2 == 3
[1] FALSE
> Rle(c(sqrt(3)^2, 3))
'numeric' Rle of length 2 with 2 runs
Lengths: 1 1
Values : 3 3
Note that base::rle() does the same:
> rle(c(sqrt(3)^2, 3))
Run Length Encoding
lengths: int [1:2] 1 1
values : num [1:2] 3 3
I can see that using a "|x1 -x2|<epsilon" criteria="" would="" in="" general="" give="" better="" compression="" (less="" runs)="" but="" then="" the="" compression="" would="" not="" be="" lossless="" as="" it="" is="" right="" now:=""> x <- c(sqrt(3)^2, 3)
> identical(as.vector(Rle(x)), x)
[1] TRUE
> identical(inverse.rle(rle(x)), x)
[1] TRUE
Also the "|x1 -x2|<epsilon" approach="" would="" introduce="" some="" subtle="" complications="" due="" to="" the="" fact="" that="" the="" criteria="" is="" not="" transitive="" anymore="" i.e.="" you="" can="" have="" |x1="" -x2|<epsilon="" and="" |x2="" -x3|<epsilon,="" without="" having="" |x1="" -x3|<epsilon.="" because="" of="" that,="" finding="" the="" runs="" becomes="" some="" kind="" of="" clustering="" problem="" with="" several="" possible="" strategies,="" some="" of="" them="" very="" simple="" but="" not="" necessarily="" with="" the="" "good="" properties".="" h.="">
> Kasper
>
>>
>> Michael
>>
>> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at="" gmail.com=""> wrote:
>>>
>>> Do we have a matrix-like object, but where the columns are Rle's?
>>>
>>> Kasper
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
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: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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12.5 years ago
Hervé Pagès
16k
0
Entering edit mode
On Wed, Jun 27, 2012 at 1:37 PM, Hervé Pagès <hpages@fhcrc.org> wrote:
> Hi Kasper,
>
> On 06/25/2012 08:56 PM, Kasper Daniel Hansen wrote:
> [...]
>
> [ side question which could be relevant in this discussion: for a
>> numeric Rle is there some notion of precision - say I have truly
>> numeric values with tons of digits, and I want to consider two
numbers
>> part of the same run if |x1 -x2|<epsilon? ]="">>
>
> The comparison of 2 doubles is done at the C level with ==, which
> AFAIK is the same as doing == in R (as long as we deal with non-NA
> and non-NaN values). See the _fill_Rle_slots_with_double_**vals()
helper
> function in IRanges/src/Rle_class.c for the details.
>
> Therefore:
>
> > all.equal(sqrt(3)^2, 3)
> [1] TRUE
> > sqrt(3)^2 == 3
> [1] FALSE
> > Rle(c(sqrt(3)^2, 3))
> 'numeric' Rle of length 2 with 2 runs
> Lengths: 1 1
> Values : 3 3
>
> Note that base::rle() does the same:
>
> > rle(c(sqrt(3)^2, 3))
> Run Length Encoding
> lengths: int [1:2] 1 1
> values : num [1:2] 3 3
>
> I can see that using a "|x1 -x2|<epsilon" criteria="" would="" in="" general=""> give better compression (less runs) but then the compression would
not
> be lossless as it is right now:
>
> > x <- c(sqrt(3)^2, 3)
> > identical(as.vector(Rle(x)), x)
> [1] TRUE
> > identical(inverse.rle(rle(x)), x)
> [1] TRUE
>
> Also the "|x1 -x2|<epsilon" approach="" would="" introduce="" some="" subtle=""> complications due to the fact that the criteria is not transitive
> anymore i.e. you can have |x1 -x2|<epsilon and="" |x2="" -x3|<epsilon,=""> without having |x1 -x3|<epsilon. because="" of="" that,="" finding="" the="" runs=""> becomes some kind of clustering problem with several possible
> strategies, some of them very simple but not necessarily with
> the "good properties".
>
>
One simple "clustering" would be to round to some fixed level of
precision.
One could multiple by some power of 10 and coerce to integer to avoid
any
floating point issues.
> H.
>
>
>
>> Kasper
>>
>>
>>> Michael
>>>
>>> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
>>> <kasperdanielhansen@gmail.com> wrote:
>>>
>>>>
>>>> Do we have a matrix-like object, but where the columns are Rle's?
>>>>
>>>> Kasper
>>>>
>>>> ______________________________**_________________
>>>> Bioconductor mailing list
>>>> Bioconductor@r-project.org
>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor="">
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.**science.biology.informatics.**condu
ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor="">
>>>>
>>>
>>>
>>>
>> ______________________________**_________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor="">
>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor="">
>>
>>
>
> --
> 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: hpages@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
>
>
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12.5 years ago
Michael Lawrence
★
11k
0
Entering edit mode
Hi Michael,
On 06/27/2012 01:58 PM, Michael Lawrence wrote:
>
>
> On Wed, Jun 27, 2012 at 1:37 PM, Hervé Pagès <hpages at="" fhcrc.org=""> <mailto:hpages at="" fhcrc.org="">> wrote:
>
> Hi Kasper,
>
> On 06/25/2012 08:56 PM, Kasper Daniel Hansen wrote:
> [...]
>
> [ side question which could be relevant in this discussion:
for a
> numeric Rle is there some notion of precision - say I have
truly
> numeric values with tons of digits, and I want to consider
two
> numbers
> part of the same run if |x1 -x2|<epsilon? ]="">
>
> The comparison of 2 doubles is done at the C level with ==,
which
> AFAIK is the same as doing == in R (as long as we deal with non-
NA
> and non-NaN values). See the
_fill_Rle_slots_with_double___vals() helper
> function in IRanges/src/Rle_class.c for the details.
>
> Therefore:
>
> > all.equal(sqrt(3)^2, 3)
> [1] TRUE
> > sqrt(3)^2 == 3
> [1] FALSE
> > Rle(c(sqrt(3)^2, 3))
> 'numeric' Rle of length 2 with 2 runs
> Lengths: 1 1
> Values : 3 3
>
> Note that base::rle() does the same:
>
> > rle(c(sqrt(3)^2, 3))
> Run Length Encoding
> lengths: int [1:2] 1 1
> values : num [1:2] 3 3
>
> I can see that using a "|x1 -x2|<epsilon" criteria="" would="" in="" general=""> give better compression (less runs) but then the compression
would not
> be lossless as it is right now:
>
> > x <- c(sqrt(3)^2, 3)
> > identical(as.vector(Rle(x)), x)
> [1] TRUE
> > identical(inverse.rle(rle(x)), x)
> [1] TRUE
>
> Also the "|x1 -x2|<epsilon" approach="" would="" introduce="" some="" subtle=""> complications due to the fact that the criteria is not
transitive
> anymore i.e. you can have |x1 -x2|<epsilon and="" |x2="" -x3|<epsilon,=""> without having |x1 -x3|<epsilon. because="" of="" that,="" finding="" the="" runs=""> becomes some kind of clustering problem with several possible
> strategies, some of them very simple but not necessarily with
> the "good properties".
>
>
> One simple "clustering" would be to round to some fixed level of
> precision. One could multiple by some power of 10 and coerce to
integer
> to avoid any floating point issues.
Like for example Rle(round(x, digits=4)). If people feel that this
would be useful, we could add the 'digits' arg to the Rle()
constructor
so the rounding is taken care of by the constructor itself. With
default
to NA for no rounding at all (like now), so the good properties are
preserved e.g. lossless compression and the fact that unique,
duplicated, is.unsorted, sort, order, rank etc (anything involving
comparison between doubles) will behave exactly the same way on x
and Rle(x) (there is code around that relies on such behavior).
Also maybe we could consider doing signif() instead of round().
Cheers,
H.
>
> H.
>
>
>
> Kasper
>
>
> Michael
>
> On Mon, Jun 25, 2012 at 8:27 PM, Kasper Daniel Hansen
> <kasperdanielhansen at="" gmail.com=""> <mailto:kasperdanielhansen at="" gmail.com="">> wrote:
>
>
> Do we have a matrix-like object, but where the
columns
> are Rle's?
>
> Kasper
>
> _________________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> <mailto:bioconductor at="" r-project.org="">
> https://stat.ethz.ch/mailman/__listinfo/bioconductor
> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">
> Search the archives:
>
http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>
<http: news.gmane.org="" gmane.science.biology.informatics.conductor="">
>
>
>
>
> _________________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org="">
> https://stat.ethz.ch/mailman/__listinfo/bioconductor
> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">
> Search the archives:
>
http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>
<http: news.gmane.org="" gmane.science.biology.informatics.conductor="">
>
>
>
> --
> 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: hpages at fhcrc.org <mailto:hpages at="" 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: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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• link
12.5 years ago
Hervé Pagès
16k
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