Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-13 Thread Hervé Pagès 

One more thing. See below...

On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote:

Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet,
which is defined in

SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R

as follows:

setAs("SummarizedExperiment", "ExpressionSet", function(from)
 as(as(from, "RangedSummarizedExperiment"), "ExpressionSet")
)

also seems to be a bit problematic, as it makes you lose your rowData/fData.



Here is an example:

## Constructing the SE similar to examples of ?SummarizedExperiment

nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),

   row.names=LETTERS[1:6])


## some rowData with simulated gene IDs

rowData <- DataFrame(EntrezID=sample(1000, 200), row.names=paste0("g",

1:200))

se <- SummarizedExperiment(assays=SimpleList(exprs=counts),

 colData=colData, rowData=rowData)

# this is how it looks

rowData(se)

DataFrame with 200 rows and 1 column
  EntrezID
 
1 289
2 476
3 608
4 998
5 684
...   ...
196   331
197   590
198   445
19995
200   129

(why did I actually lost the rownames g1-g200 here?)


Your rownames were moved to the names of the object:

> head(names(se))
[1] "g1" "g2" "g3" "g4" "g5" "g6"

The rowData() accessor (like the mcols() accessor, note that rowData()
is just an alias for mcols) does not restore them by default, unless
you use 'use.names=TRUE'.

> rowData(se, use.names=TRUE)
DataFrame with 200 rows and 1 column
  EntrezID
 
g1 616
g2  45
g3 944
g4 632
g5 270
......
g196   827
g197   943
g198   291
g199   432
g200   106

All Vector derivatives do that (e.g. GRanges), not just
SummarizedExperiment.

The reason for this design is that the rownames must be unique
(this is a base R requirement). By moving them from the DataFrame
containing the metadata columns to the names of the object, Vector
derivatives can be subsetted in a way that repeat some of their
elements. If the rownames were on the DataFrame containing the
metadata columns, these subsetting operations wouldn't be
possible.

Hope this makes sense,
H.




## Coercing to Expression makes me losing the rowData/fData

eset <- as(se, "ExpressionSet")
fData(eset)

data frame with 0 columns and 200 rows


## So where is the problem?
## Apparently in the coercion
##from SummarizedExperiment to RangedSummarizedExperiment

rse <- as(se, "RangedSummarizedExperiment")
rowData(rse)

DataFrame with 200 rows and 0 columns




--
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...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-13 Thread Hervé Pagès 

Hi Ludwig,

Excellent catch! Thanks for the report.

This should be fixed in SummarizedExperiment release (1.6.4) and devel
(1.7.7).

Cheers,
H.

On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote:

Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet,
which is defined in

SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R

as follows:

setAs("SummarizedExperiment", "ExpressionSet", function(from)
 as(as(from, "RangedSummarizedExperiment"), "ExpressionSet")
)

also seems to be a bit problematic, as it makes you lose your rowData/fData.



Here is an example:

## Constructing the SE similar to examples of ?SummarizedExperiment

nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),

   row.names=LETTERS[1:6])


## some rowData with simulated gene IDs

rowData <- DataFrame(EntrezID=sample(1000, 200), row.names=paste0("g",

1:200))

se <- SummarizedExperiment(assays=SimpleList(exprs=counts),

 colData=colData, rowData=rowData)

# this is how it looks

rowData(se)

DataFrame with 200 rows and 1 column
  EntrezID
 
1 289
2 476
3 608
4 998
5 684
...   ...
196   331
197   590
198   445
19995
200   129

(why did I actually lost the rownames g1-g200 here?)


## Coercing to Expression makes me losing the rowData/fData

eset <- as(se, "ExpressionSet")
fData(eset)

data frame with 0 columns and 200 rows


## So where is the problem?
## Apparently in the coercion
##from SummarizedExperiment to RangedSummarizedExperiment

rse <- as(se, "RangedSummarizedExperiment")
rowData(rse)

DataFrame with 200 rows and 0 columns




--
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...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Kasper Daniel Hansen 
I see how an eSet maps to a SummarizedExperiment; one can look at the
assays in the object.  I agree with Levi/Herve that this is the natural
(correct) choice.  It is less clear how you get the ranges for a
RangedSummarizedExperiment without making assumptions.

On Mon, Sep 11, 2017 at 8:09 PM, Hervé Pagès  wrote:

> I don't know the reasons behind this choice, I didn't implement
> these methods. It would make sense to have these coercions defined
> for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
> signatures if they only access the eSet part of the object.
> I'll look into this.
>
> H.
>
> On 09/11/2017 04:50 PM, Levi Waldron wrote:
>
>> Thanks Ludwig and Kasper. This old presentation from Martin also helped me
>> a lot:
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bio
>> conductor.org_packages_devel_bioc_vignettes_Biobase_inst_
>> doc_BiobaseDevelopment.pdf=DwIGaQ=eRAMFD45gAfqt84VtBcfh
>> Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s44znXbg9V
>> OxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=C-oKupgUQZm6PA2e1IWSKKQq
>> PsQIy4uTGUg_CSvBeq4=
>>
>> But I still wonder, why provide the coercion for ExpressionSet, if
>> providing it for eSet would work not only for ExpressionSet but for
>> everything else derived from eSet? The coercion function seems to work
>> fine
>> on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from)
>> )
>>   seems to work regardless of the storage mode}:
>>
>> library(Biobase)> library(SummarizedExperiment)>
>>> example("NChannelSet-class", echo=FALSE)> class(obj)[1] "NChannelSet"
>>>
>> attr(,"package")
>> [1] "Biobase"> is(obj, "eSet")[1] TRUE
>>
>> storageMode(obj)[1] "lockedEnvironment"
>>>
>>
>> makeSummarizedExperimentFromExpressionSet(obj) class:
>>>
>> RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData
>> annotation
>> protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
>> colnames(3): A B C colData names(3): ChannelRData ChannelGData
>> ChannelRAndG
>>
>> as(obj, "RangedSummarizedExperiment")
>>>
>>
>> Error in as(obj, "RangedSummarizedExperiment") :
>>no method or default for coercing “NChannelSet” to
>> “RangedSummarizedExperiment”
>>
>>
>>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s4
>> 4znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=qKI2hqP0ltgK5_
>> LBtVFG6Va-8XAUuGwbXp9eKUfulXs=
>>
>>
> --
> 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...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Hervé Pagès 

I don't know the reasons behind this choice, I didn't implement
these methods. It would make sense to have these coercions defined
for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
signatures if they only access the eSet part of the object.
I'll look into this.

H.

On 09/11/2017 04:50 PM, Levi Waldron wrote:

Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_devel_bioc_vignettes_Biobase_inst_doc_BiobaseDevelopment.pdf=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s44znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=C-oKupgUQZm6PA2e1IWSKKQqPsQIy4uTGUg_CSvBeq4=

But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for ExpressionSet but for
everything else derived from eSet? The coercion function seems to work fine
on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from))
  seems to work regardless of the storage mode}:


library(Biobase)> library(SummarizedExperiment)> example("NChannelSet-class", 
echo=FALSE)> class(obj)[1] "NChannelSet"

attr(,"package")
[1] "Biobase"> is(obj, "eSet")[1] TRUE


storageMode(obj)[1] "lockedEnvironment"



makeSummarizedExperimentFromExpressionSet(obj) class:

RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData annotation
protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
colnames(3): A B C colData names(3): ChannelRData ChannelGData ChannelRAndG


as(obj, "RangedSummarizedExperiment")


Error in as(obj, "RangedSummarizedExperiment") :
   no method or default for coercing “NChannelSet” to
“RangedSummarizedExperiment”





[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s44znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=qKI2hqP0ltgK5_LBtVFG6Va-8XAUuGwbXp9eKUfulXs=



--
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...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Levi Waldron 
Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:

https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf

But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for ExpressionSet but for
everything else derived from eSet? The coercion function seems to work fine
on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from))
 seems to work regardless of the storage mode}:

> library(Biobase)> library(SummarizedExperiment)> example("NChannelSet-class", 
> echo=FALSE)> class(obj)[1] "NChannelSet"
attr(,"package")
[1] "Biobase"> is(obj, "eSet")[1] TRUE

> storageMode(obj)[1] "lockedEnvironment"

> makeSummarizedExperimentFromExpressionSet(obj) class:
RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData annotation
protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
colnames(3): A B C colData names(3): ChannelRData ChannelGData ChannelRAndG

> as(obj, "RangedSummarizedExperiment")

Error in as(obj, "RangedSummarizedExperiment") :
  no method or default for coercing “NChannelSet” to
“RangedSummarizedExperiment”

>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Kasper Daniel Hansen 
An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay.
That makes no sense for example for methylation where we have (say)
Green/Red assays or Meth/Unmeth assays (or transformations of these).

Best,
Kasper

On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:

> Concerning 1) Why have some developers chosen to extend eSet instead of
> ExpressionSet:
>
> As far as I understand it, ExpressionSet was thought to exclusively
> represent a microarray experiment (MIAME = Minimum Information About a
> Microarray Experiment).
>
> Thus, back in the days when more and more people started using RNA-seq and
> there was no SummarizedExperiment, developers extended eSet with e.g.
> assayData slots called `counts` instead of `exprs` to represent RNA-seq
> data.
>
>
> > On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès 
> > wrote:
> >
> >> Hi,
> >>
> >> I added coercion from ExpressionSet to SummarizedExperiment in
> >> SummarizedExperiment 1.7.6.
> >>
> >
> > Thank you Hervé!
> >
> >
> >> The current behavior of the SummarizedExperiment() constructor
> >> when called on a ExpressionSet object doesn't make much sense to
> >> me. I'd rather have it consistent with what the coercion does.
> >> Will fix it.
> >>
> >
> > Thank you, again.
> >
> > A couple more questions while I'm at it, that may expose the limitations
> > in
> > my understanding of inheritance and project history... 1) Why have some
> > developers chosen to extend eSet instead of ExpressionSet (definition
> >  536f137165ca08b3be22819e51e055b3e7afe86d/R/DataClasses.R#L166>),
> > and 2) why are these coercion methods developed for ExpressionSet rather
> > than eSet? Wouldn't an eSet coercion method be preferable because it
> would
> > cover ExpressionSet as well as all the classes that extend eSet?
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Dr. Ludwig Geistlinger
> eMail: ludwig.geistlin...@bio.ifi.lmu.de
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Ludwig Geistlinger 
Concerning 1) Why have some developers chosen to extend eSet instead of
ExpressionSet:

As far as I understand it, ExpressionSet was thought to exclusively
represent a microarray experiment (MIAME = Minimum Information About a
Microarray Experiment).

Thus, back in the days when more and more people started using RNA-seq and
there was no SummarizedExperiment, developers extended eSet with e.g.
assayData slots called `counts` instead of `exprs` to represent RNA-seq
data.


> On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès 
> wrote:
>
>> Hi,
>>
>> I added coercion from ExpressionSet to SummarizedExperiment in
>> SummarizedExperiment 1.7.6.
>>
>
> Thank you Hervé!
>
>
>> The current behavior of the SummarizedExperiment() constructor
>> when called on a ExpressionSet object doesn't make much sense to
>> me. I'd rather have it consistent with what the coercion does.
>> Will fix it.
>>
>
> Thank you, again.
>
> A couple more questions while I'm at it, that may expose the limitations
> in
> my understanding of inheritance and project history... 1) Why have some
> developers chosen to extend eSet instead of ExpressionSet (definition
> ),
> and 2) why are these coercion methods developed for ExpressionSet rather
> than eSet? Wouldn't an eSet coercion method be preferable because it would
> cover ExpressionSet as well as all the classes that extend eSet?
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Levi Waldron 
On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès  wrote:

> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>

Thank you Hervé!


> The current behavior of the SummarizedExperiment() constructor
> when called on a ExpressionSet object doesn't make much sense to
> me. I'd rather have it consistent with what the coercion does.
> Will fix it.
>

Thank you, again.

A couple more questions while I'm at it, that may expose the limitations in
my understanding of inheritance and project history... 1) Why have some
developers chosen to extend eSet instead of ExpressionSet (definition
),
and 2) why are these coercion methods developed for ExpressionSet rather
than eSet? Wouldn't an eSet coercion method be preferable because it would
cover ExpressionSet as well as all the classes that extend eSet?

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Hervé Pagès 

Hi,

I added coercion from ExpressionSet to SummarizedExperiment in
SummarizedExperiment 1.7.6.

The current behavior of the SummarizedExperiment() constructor
when called on a ExpressionSet object doesn't make much sense to
me. I'd rather have it consistent with what the coercion does.
Will fix it.

Cheers,
H.

On 09/11/2017 09:58 AM, Michael Lawrence wrote:

It's probably good keeping coercion and construction distinct,
although we have violated that recently with GRanges(). It now
attempts to coerce its first argument to a GRanges. Don't want to
derail the discussion, but it's another data point.

Michael

On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
 wrote:

On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:


I guess we discussed this with Davide Risso @Bioc2017 in the
MultiAssayExperiment workshop.


SummarizedExperiment(mouseData)


puts the eSet (rather counterintuitively) into `assays` of
`SummarizedExperiment`, it does not really coerce it to
SummarizedExperiment, eg. `fData` and `pData` are not accordingly
transferred to colData and rowData.



Right, I had forgotten about that - this isn't a coercion but a
construction, which should be obvious from the use of a constructor
function. This behavior is intuitive if you remember that
SummarizedExperiment(assays, ...) is a constructor that accepts as assays
any object or list of objects supporting square bracket matrix-like
subsetting. Sorry for my brain hiccup there.



While I can understand that this is by design of `SummarizedExperiment`, I
really wonder whether there are use cases where somebody would like to put
an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
would like to coerce it that way.

Furthermore, if you would indeed like to have several `ExpressionSet`s in
a `SummarizedExperiment`, haven't you already arrived at a scenario where
use of `MultiAssayExperiment` is indicated?



I think the behavior of the constructor SummarizedExperiment() here is
correct and expected, the issue here is that we're actually looking for
coercion methods.

 [[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=heIkyXEvaJsN7zonHbzq6mmEiCHM2Ke_vMIGj7UTjx4=y4N3gOdF0D5AcrbAJZR_6Ne8WxR26lIdwbIK_L1KwrA=


___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=heIkyXEvaJsN7zonHbzq6mmEiCHM2Ke_vMIGj7UTjx4=y4N3gOdF0D5AcrbAJZR_6Ne8WxR26lIdwbIK_L1KwrA=



--
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...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Michael Lawrence 
It's probably good keeping coercion and construction distinct,
although we have violated that recently with GRanges(). It now
attempts to coerce its first argument to a GRanges. Don't want to
derail the discussion, but it's another data point.

Michael

On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
 wrote:
> On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
> ludwig.geistlin...@bio.ifi.lmu.de> wrote:
>
>> I guess we discussed this with Davide Risso @Bioc2017 in the
>> MultiAssayExperiment workshop.
>>
>> > SummarizedExperiment(mouseData)
>>
>> puts the eSet (rather counterintuitively) into `assays` of
>> `SummarizedExperiment`, it does not really coerce it to
>> SummarizedExperiment, eg. `fData` and `pData` are not accordingly
>> transferred to colData and rowData.
>>
>
> Right, I had forgotten about that - this isn't a coercion but a
> construction, which should be obvious from the use of a constructor
> function. This behavior is intuitive if you remember that
> SummarizedExperiment(assays, ...) is a constructor that accepts as assays
> any object or list of objects supporting square bracket matrix-like
> subsetting. Sorry for my brain hiccup there.
>
>
>> While I can understand that this is by design of `SummarizedExperiment`, I
>> really wonder whether there are use cases where somebody would like to put
>> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
>> would like to coerce it that way.
>>
>> Furthermore, if you would indeed like to have several `ExpressionSet`s in
>> a `SummarizedExperiment`, haven't you already arrived at a scenario where
>> use of `MultiAssayExperiment` is indicated?
>>
>
> I think the behavior of the constructor SummarizedExperiment() here is
> correct and expected, the issue here is that we're actually looking for
> coercion methods.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Levi Waldron 
On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:

> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `SummarizedExperiment`, it does not really coerce it to
> SummarizedExperiment, eg. `fData` and `pData` are not accordingly
> transferred to colData and rowData.
>

Right, I had forgotten about that - this isn't a coercion but a
construction, which should be obvious from the use of a constructor
function. This behavior is intuitive if you remember that
SummarizedExperiment(assays, ...) is a constructor that accepts as assays
any object or list of objects supporting square bracket matrix-like
subsetting. Sorry for my brain hiccup there.


> While I can understand that this is by design of `SummarizedExperiment`, I
> really wonder whether there are use cases where somebody would like to put
> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
> would like to coerce it that way.
>
> Furthermore, if you would indeed like to have several `ExpressionSet`s in
> a `SummarizedExperiment`, haven't you already arrived at a scenario where
> use of `MultiAssayExperiment` is indicated?
>

I think the behavior of the constructor SummarizedExperiment() here is
correct and expected, the issue here is that we're actually looking for
coercion methods.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Ludwig Geistlinger 
I guess we discussed this with Davide Risso @Bioc2017 in the
MultiAssayExperiment workshop.

> SummarizedExperiment(mouseData)

puts the eSet (rather counterintuitively) into `assays` of
`SummarizedExperiment`, it does not really coerce it to
SummarizedExperiment, eg. `fData` and `pData` are not accordingly
transferred to colData and rowData.

While I can understand that this is by design of `SummarizedExperiment`, I
really wonder whether there are use cases where somebody would like to put
an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
would like to coerce it that way.

Furthermore, if you would indeed like to have several `ExpressionSet`s in
a `SummarizedExperiment`, haven't you already arrived at a scenario where
use of `MultiAssayExperiment` is indicated?


> Thanks Martin! I see the RangedSummarizedExperiment coercion method works
> when there are no mappable ranges (for example curatedMetagenomicData
> ExpressionSet objects), although the rowRanges is a GRangesList of empty
> elements. It might be worth also having a SummarizedExperiment coercion
> method it it's not a problematic or big job. And now I suppose I can ask
> the question I *really* wanted to know, which is why can't I coerce an
> object that extends eSet? I can still use the SummarizedExperiment()
> constructor, but for example:
>
>> library(metagenomeSeq)> data(mouseData)> class(mouseData)[1]
>> "MRexperiment"
> attr(,"package")
> [1] "metagenomeSeq"> is(mouseData, "ExpressionSet")[1] FALSE>
> is(mouseData, "eSet")[1] TRUE
>
>> SummarizedExperiment(mouseData)class: SummarizedExperiment
> dim: 10172 139
> metadata(0):
> assays(1): ''
> rownames(10172): Prevotellaceae:1 Lachnospiraceae:1 ... Bryantella:103
>   Parabacteroides:956
> rowData names(0):
> colnames(139): PM1:20080107 PM1:20080108 ... PM9:20080225 PM9:20080303
> colData names(0):
>
>> as(mouseData, "RangedSummarizedExperiment") Error in as(mouseData,
> "RangedSummarizedExperiment") : no method or default for coercing
> “MRexperiment” to “RangedSummarizedExperiment” > as(mouseData,
> "SummarizedExperiment") Error in as(mouseData, "SummarizedExperiment") :
> no
> method or default for coercing “MRexperiment” to
> “SummarizedExperiment” > as(mouseData,
> "ExpressionSet") Error in updateOldESet(from, "ExpressionSet") : no slot
> of
> name "pData" for this object of class "AnnotatedDataFrame" >
>
>
>
>
> On Mon, Sep 11, 2017 at 6:58 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
>> On 09/10/2017 08:38 PM, Levi Waldron wrote:
>>
>>> I just dug up this old thread because I realized we still don't have a
>>> coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since
>>> we
>>>
>>
>> try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
>> ?makeSummarizedExperimentFromExpressionSet
>>
>> do have SummarizedExperiment(sample.ExpressionSet), could the coercion
>>> method also be added easily?
>>>
>>> library(Biobase) > library(SummarizedExperiment) >

>>> example("ExpressionSet")
>>>
>>> SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment

>>> dim: 500 26
>>> metadata(0):
>>> assays(1): ''
>>> rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
>>> rowData names(0):
>>> colnames(26): A B ... Y Z
>>> colData names(0):> as(sample.ExpressionSet,
>>> "SummarizedExperiment")Error in as(sample.ExpressionSet,
>>> "SummarizedExperiment") :
>>>no method or default for coercing “ExpressionSet” to
>>> “SummarizedExperiment”
>>>
>>> sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)

>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 16.04.3 LTS
>>>
>>> Matrix products: default
>>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
>>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>>> LC_TIME=en_US.UTF-8
>>>   [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
>>> LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>>> LC_ADDRESS=C
>>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>>> LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4parallel  stats graphics  grDevices utils
>>> datasets  methods   base
>>>
>>> other attached packages:
>>> [1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
>>> matrixStats_0.52.2
>>> [4] GenomicRanges_1.29.6   GenomeInfoDb_1.13.4
>>> IRanges_2.11.7
>>> [7] S4Vectors_0.15.5   Biobase_2.37.2
>>> BiocGenerics_0.23.0
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] lattice_0.20-35 bitops_1.0-6grid_3.4.0
>>>   [4] zlibbioc_1.23.0 XVector_0.17.0  Matrix_1.2-11
>>>   [7] tools_3.4.0 RCurl_1.95-4.8  compiler_3.4.0
>>> [10] GenomeInfoDbData_0.99.1
>>>
>>>

>>> On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès 
>>> wrote:
>>>
>>> Hi,

 On 09/20/2014 11:14 AM, Martin Morgan wrote:

 On

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Levi Waldron 
Thanks Martin! I see the RangedSummarizedExperiment coercion method works
when there are no mappable ranges (for example curatedMetagenomicData
ExpressionSet objects), although the rowRanges is a GRangesList of empty
elements. It might be worth also having a SummarizedExperiment coercion
method it it's not a problematic or big job. And now I suppose I can ask
the question I *really* wanted to know, which is why can't I coerce an
object that extends eSet? I can still use the SummarizedExperiment()
constructor, but for example:

> library(metagenomeSeq)> data(mouseData)> class(mouseData)[1] "MRexperiment"
attr(,"package")
[1] "metagenomeSeq"> is(mouseData, "ExpressionSet")[1] FALSE>
is(mouseData, "eSet")[1] TRUE

> SummarizedExperiment(mouseData)class: SummarizedExperiment
dim: 10172 139
metadata(0):
assays(1): ''
rownames(10172): Prevotellaceae:1 Lachnospiraceae:1 ... Bryantella:103
  Parabacteroides:956
rowData names(0):
colnames(139): PM1:20080107 PM1:20080108 ... PM9:20080225 PM9:20080303
colData names(0):

> as(mouseData, "RangedSummarizedExperiment") Error in as(mouseData,
"RangedSummarizedExperiment") : no method or default for coercing
“MRexperiment” to “RangedSummarizedExperiment” > as(mouseData,
"SummarizedExperiment") Error in as(mouseData, "SummarizedExperiment") : no
method or default for coercing “MRexperiment” to
“SummarizedExperiment” > as(mouseData,
"ExpressionSet") Error in updateOldESet(from, "ExpressionSet") : no slot of
name "pData" for this object of class "AnnotatedDataFrame" >




On Mon, Sep 11, 2017 at 6:58 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 09/10/2017 08:38 PM, Levi Waldron wrote:
>
>> I just dug up this old thread because I realized we still don't have a
>> coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
>>
>
> try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
> ?makeSummarizedExperimentFromExpressionSet
>
> do have SummarizedExperiment(sample.ExpressionSet), could the coercion
>> method also be added easily?
>>
>> library(Biobase) > library(SummarizedExperiment) >
>>>
>> example("ExpressionSet")
>>
>> SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment
>>>
>> dim: 500 26
>> metadata(0):
>> assays(1): ''
>> rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
>> rowData names(0):
>> colnames(26): A B ... Y Z
>> colData names(0):> as(sample.ExpressionSet,
>> "SummarizedExperiment")Error in as(sample.ExpressionSet,
>> "SummarizedExperiment") :
>>no method or default for coercing “ExpressionSet” to
>> “SummarizedExperiment”
>>
>> sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)
>>>
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.3 LTS
>>
>> Matrix products: default
>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8
>>   [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
>> LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>> LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4parallel  stats graphics  grDevices utils
>> datasets  methods   base
>>
>> other attached packages:
>> [1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
>> matrixStats_0.52.2
>> [4] GenomicRanges_1.29.6   GenomeInfoDb_1.13.4
>> IRanges_2.11.7
>> [7] S4Vectors_0.15.5   Biobase_2.37.2
>> BiocGenerics_0.23.0
>>
>> loaded via a namespace (and not attached):
>>   [1] lattice_0.20-35 bitops_1.0-6grid_3.4.0
>>   [4] zlibbioc_1.23.0 XVector_0.17.0  Matrix_1.2-11
>>   [7] tools_3.4.0 RCurl_1.95-4.8  compiler_3.4.0
>> [10] GenomeInfoDbData_0.99.1
>>
>>
>>>
>> On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès  wrote:
>>
>> Hi,
>>>
>>> On 09/20/2014 11:14 AM, Martin Morgan wrote:
>>>
>>> On 09/20/2014 10:43 AM, Sean Davis wrote:

 Hi, Vince.
>
> Looks like a good start.  I'd probably pull all the assays from
> ExpressionSet into SummarizedExperiment as the default, avoiding data
> coercion methods that are unnecessarily lossy.  Also, as it stands, the
> assayname argument is not used anyway?
>
>
 I think there will be some resistance to uniting the 'Biobase' and
 'IRanges' realms under 'GenomicRanges';


>>> This coercion method could be defined (1) in Biobase (where
>>> ExpressionSet is defined), (2) in GenomicRanges (where
>>> SummarizedExperiment is defined), or (3) in a package that
>>> depends on Biobase and GenomicRanges.
>>>
>>> Since it's probably undesirable to make Biobase depend on GenomicRanges
>>> or vice-versa, we would need to use Suggests for (1) or (2). That
>>> means we would get a note like this at installation time:
>>>
>>>   ** preparing package for lazy loading
>>>   in method for

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Martin Morgan 

On 09/10/2017 08:38 PM, Levi Waldron wrote:

I just dug up this old thread because I realized we still don't have a
coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we


try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see 
?makeSummarizedExperimentFromExpressionSet



do have SummarizedExperiment(sample.ExpressionSet), could the coercion
method also be added easily?


library(Biobase) > library(SummarizedExperiment) >

example("ExpressionSet")


SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment

dim: 500 26
metadata(0):
assays(1): ''
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(0):> as(sample.ExpressionSet,
"SummarizedExperiment")Error in as(sample.ExpressionSet,
"SummarizedExperiment") :
   no method or default for coercing “ExpressionSet” to “SummarizedExperiment”


sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
LC_TIME=en_US.UTF-8
  [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils
datasets  methods   base

other attached packages:
[1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
matrixStats_0.52.2
[4] GenomicRanges_1.29.6   GenomeInfoDb_1.13.4
IRanges_2.11.7
[7] S4Vectors_0.15.5   Biobase_2.37.2
BiocGenerics_0.23.0

loaded via a namespace (and not attached):
  [1] lattice_0.20-35 bitops_1.0-6grid_3.4.0
  [4] zlibbioc_1.23.0 XVector_0.17.0  Matrix_1.2-11
  [7] tools_3.4.0 RCurl_1.95-4.8  compiler_3.4.0
[10] GenomeInfoDbData_0.99.1





On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès  wrote:


Hi,

On 09/20/2014 11:14 AM, Martin Morgan wrote:


On 09/20/2014 10:43 AM, Sean Davis wrote:


Hi, Vince.

Looks like a good start.  I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy.  Also, as it stands, the
assayname argument is not used anyway?



I think there will be some resistance to uniting the 'Biobase' and
'IRanges' realms under 'GenomicRanges';



This coercion method could be defined (1) in Biobase (where
ExpressionSet is defined), (2) in GenomicRanges (where
SummarizedExperiment is defined), or (3) in a package that
depends on Biobase and GenomicRanges.

Since it's probably undesirable to make Biobase depend on GenomicRanges
or vice-versa, we would need to use Suggests for (1) or (2). That
means we would get a note like this at installation time:

  ** preparing package for lazy loading
  in method for ‘coerce’ with signature ‘"ExpressionSet","SummarizedEx
periment"’:
  no definition for class “SummarizedExperiment”

Not very clean but it works.

(3) is a cleaner solution but then the coercion method would
not necessarily be available to the user when s/he needs it (unless
s/he knows what extra package to load). The obvious advantage of
putting the method in Biobase is that if a user has an ExpressionSet,
then s/he necessarily has Biobase attached and the method is already
in her/his search path.

Another solution would be (4) to move SummarizedExperiment somewhere
else. That would be in a package that depends on GenomicRanges and
Biobase, and the coercion method would be defined there.

H.


considerable effort has gone in

to making a rational hierarchy of package dependencies [perhaps Herve
will point to some of his ASCII art on the subject].

I have some recollection of (recent) discussion related to this topic in
the DESeq2 realm, but am drawing a blank; presumably Michael or Wolfgang
or ... will chime in.

Martin



Sean


On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey

wrote:

do we have a facility for this?


if not, we have

https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R

https://github.com/vjcitn/biocMultiAssay/blob/master/man/coe
rce-methods.Rd


it occurred to me that we might want something like this in
GenomicRanges
(that's where SummarizedExperiment is managed, right?) and I will add it
if there are no objections

the arguments are currently

   assayname = "exprs",# for naming SimpleList element
   fngetter =
 function(z) rownames(exprs(z)),   # extract usable
feature names
   annDbGetter =
function(z) {
clnanno = sub(".db", "", annotation(z))
stopifnot(require(paste0(annotation(z), ".db"),
character.only=TRUE) )

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-10 Thread Levi Waldron 
I just dug up this old thread because I realized we still don't have a
coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
do have SummarizedExperiment(sample.ExpressionSet), could the coercion
method also be added easily?

> library(Biobase) > library(SummarizedExperiment) >
example("ExpressionSet")

> SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment
dim: 500 26
metadata(0):
assays(1): ''
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(0):> as(sample.ExpressionSet,
"SummarizedExperiment")Error in as(sample.ExpressionSet,
"SummarizedExperiment") :
  no method or default for coercing “ExpressionSet” to “SummarizedExperiment”

> sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils
datasets  methods   base

other attached packages:
[1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
matrixStats_0.52.2
[4] GenomicRanges_1.29.6   GenomeInfoDb_1.13.4
IRanges_2.11.7
[7] S4Vectors_0.15.5   Biobase_2.37.2
BiocGenerics_0.23.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-35 bitops_1.0-6grid_3.4.0
 [4] zlibbioc_1.23.0 XVector_0.17.0  Matrix_1.2-11
 [7] tools_3.4.0 RCurl_1.95-4.8  compiler_3.4.0
[10] GenomeInfoDbData_0.99.1

>

On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès  wrote:

> Hi,
>
> On 09/20/2014 11:14 AM, Martin Morgan wrote:
>
>> On 09/20/2014 10:43 AM, Sean Davis wrote:
>>
>>> Hi, Vince.
>>>
>>> Looks like a good start.  I'd probably pull all the assays from
>>> ExpressionSet into SummarizedExperiment as the default, avoiding data
>>> coercion methods that are unnecessarily lossy.  Also, as it stands, the
>>> assayname argument is not used anyway?
>>>
>>
>> I think there will be some resistance to uniting the 'Biobase' and
>> 'IRanges' realms under 'GenomicRanges';
>>
>
> This coercion method could be defined (1) in Biobase (where
> ExpressionSet is defined), (2) in GenomicRanges (where
> SummarizedExperiment is defined), or (3) in a package that
> depends on Biobase and GenomicRanges.
>
> Since it's probably undesirable to make Biobase depend on GenomicRanges
> or vice-versa, we would need to use Suggests for (1) or (2). That
> means we would get a note like this at installation time:
>
>  ** preparing package for lazy loading
>  in method for ‘coerce’ with signature ‘"ExpressionSet","SummarizedEx
> periment"’:
>  no definition for class “SummarizedExperiment”
>
> Not very clean but it works.
>
> (3) is a cleaner solution but then the coercion method would
> not necessarily be available to the user when s/he needs it (unless
> s/he knows what extra package to load). The obvious advantage of
> putting the method in Biobase is that if a user has an ExpressionSet,
> then s/he necessarily has Biobase attached and the method is already
> in her/his search path.
>
> Another solution would be (4) to move SummarizedExperiment somewhere
> else. That would be in a package that depends on GenomicRanges and
> Biobase, and the coercion method would be defined there.
>
> H.
>
>
> considerable effort has gone in
>> to making a rational hierarchy of package dependencies [perhaps Herve
>> will point to some of his ASCII art on the subject].
>>
>> I have some recollection of (recent) discussion related to this topic in
>> the DESeq2 realm, but am drawing a blank; presumably Michael or Wolfgang
>> or ... will chime in.
>>
>> Martin
>>
>>
>>> Sean
>>>
>>>
>>> On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey
>>> 
>>> wrote:
>>>
>>> do we have a facility for this?

 if not, we have

 https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R

 https://github.com/vjcitn/biocMultiAssay/blob/master/man/coe
 rce-methods.Rd


 it occurred to me that we might want something like this in
 GenomicRanges
 (that's where SummarizedExperiment is managed, right?) and I will add it
 if there are no objections

 the arguments are currently

   assayname = "exprs",# for naming SimpleList element
   fngetter =
 function(z) rownames(exprs(z)),   # extract usable
 feature names
   annDbGetter =
function(z) {
clnanno = sub(".db", "", annotation(z))

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2014-09-20 Thread Sean Davis 
Hi, Vince.

Looks like a good start.  I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy.  Also, as it stands, the
assayname argument is not used anyway?

Sean


On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey st...@channing.harvard.edu
wrote:

 do we have a facility for this?

 if not, we have

 https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R

 https://github.com/vjcitn/biocMultiAssay/blob/master/man/coerce-methods.Rd

 it occurred to me that we might want something like this in GenomicRanges
 (that's where SummarizedExperiment is managed, right?) and I will add it
 if there are no objections

 the arguments are currently

  assayname = exprs,# for naming SimpleList element
  fngetter =
function(z) rownames(exprs(z)),   # extract usable feature names
  annDbGetter =
   function(z) {
   clnanno = sub(.db, , annotation(z))
   stopifnot(require(paste0(annotation(z), .db),
 character.only=TRUE) )
   get(paste0(annotation(z), .db))  # obtain resource for
 mapping feature names to coordinates
   },
  probekeytype = PROBEID,   # chipDb field to use
  duphandler = function(z) {# action to take to process duplicated
 features
   if (any(isd - duplicated(z[,PROBEID])))
   return(z[!isd,,drop=FALSE])
   z
   },
  signIsStrand = TRUE,   # verify that signs of addresses define strand
  ucsdChrnames = TRUE# prefix 'chr' to chromosome token

 [[alternative HTML version deleted]]

 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel


[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2014-09-20 Thread Martin Morgan 

On 09/20/2014 10:43 AM, Sean Davis wrote:

Hi, Vince.

Looks like a good start.  I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy.  Also, as it stands, the
assayname argument is not used anyway?


I think there will be some resistance to uniting the 'Biobase' and 'IRanges' 
realms under 'GenomicRanges'; considerable effort has gone in to making a 
rational hierarchy of package dependencies [perhaps Herve will point to some of 
his ASCII art on the subject].


I have some recollection of (recent) discussion related to this topic in the 
DESeq2 realm, but am drawing a blank; presumably Michael or Wolfgang or ... will 
chime in.


Martin



Sean


On Sat, Sep 20, 2014 at 10:38 AM, Vincent Carey st...@channing.harvard.edu
wrote:


do we have a facility for this?

if not, we have

https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R

https://github.com/vjcitn/biocMultiAssay/blob/master/man/coerce-methods.Rd

it occurred to me that we might want something like this in GenomicRanges
(that's where SummarizedExperiment is managed, right?) and I will add it
if there are no objections

the arguments are currently

  assayname = exprs,# for naming SimpleList element
  fngetter =
function(z) rownames(exprs(z)),   # extract usable feature names
  annDbGetter =
   function(z) {
   clnanno = sub(.db, , annotation(z))
   stopifnot(require(paste0(annotation(z), .db),
character.only=TRUE) )
   get(paste0(annotation(z), .db))  # obtain resource for
mapping feature names to coordinates
   },
  probekeytype = PROBEID,   # chipDb field to use
  duphandler = function(z) {# action to take to process duplicated
features
   if (any(isd - duplicated(z[,PROBEID])))
   return(z[!isd,,drop=FALSE])
   z
   },
  signIsStrand = TRUE,   # verify that signs of addresses define strand
  ucsdChrnames = TRUE# prefix 'chr' to chromosome token

 [[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel




--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel