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Question: On extending class ExpressionSet
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gravatar for Renaud Gaujoux
6.9 years ago by
Renaud Gaujoux160 wrote:
Hi, I am trying to extend class ExpressionSet in a very simple way to add an extra slot. Now suppose I have a valid ExpressionSet object, I want to create an object of class 'A' as follows (this always worked with other S4 classes I defined): library(Biobase) setClass('A', representation(extraslot='list'), contains='ExpressionSet') eset <- new('ExpressionSet') new('A', eset) # this throws the error: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "annotatedDataFrameFrom", for signature "ExpressionSet" #Note: this also does not work with a non-empty ExpressionSet object. Is this normal? Is there a specific way to extend the class ExpressionSet? The classes I found that extend ExpressionSet add an extra element in assayData, and from what I saw it requires defining an initialize method to pass all the standard parameters to the underlying ExpressionSet object (exprs, phenoData, featureData, etc...) Thank you for any insight on the matter. Renaud sessionInfo: R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_ZA.utf8 LC_NUMERIC=C LC_TIME=en_ZA.utf8 LC_COLLATE=en_ZA.utf8 LC_MONETARY=C LC_MESSAGES=en_ZA.utf8 LC_PAPER=en_ZA.utf8 [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_ZA.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.8.0 ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}}
ADD COMMENTlink modified 6.9 years ago by Martin Morgan ♦♦ 20k • written 6.9 years ago by Renaud Gaujoux160
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gravatar for Martin Morgan
6.9 years ago by
Martin Morgan ♦♦ 20k
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Martin Morgan ♦♦ 20k wrote:
On 12/15/2010 09:42 AM, Renaud Gaujoux wrote: > Hi, > > I am trying to extend class ExpressionSet in a very simple way to add an > extra slot. > Now suppose I have a valid ExpressionSet object, I want to create an > object of class 'A' as follows (this always worked with other S4 classes > I defined): > > library(Biobase) > setClass('A', representation(extraslot='list'), contains='ExpressionSet') > eset <- new('ExpressionSet') > new('A', eset) > > # this throws the error: > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function > "annotatedDataFrameFrom", for signature "ExpressionSet" > #Note: this also does not work with a non-empty ExpressionSet object. > > Is this normal? Is there a specific way to extend the class ExpressionSet? > The classes I found that extend ExpressionSet add an extra element in > assayData, and from what I saw it requires defining an initialize method > to pass all the standard parameters to the underlying ExpressionSet > object (exprs, phenoData, featureData, etc...) Hi Renaud -- This is an unfortunate consequence of the 'initialize' method that your class inherits from ExpressionSet. 'new' uses the prototype of 'A' to create .Object, and then passes .Object and other arguments to 'new' down to 'initialize'. The 'initialize' method inherited from ExpressionSet is in part > head(selectMethod(initialize, 'A')) 1 structure(function (.Object, ...) 2 { 3 .local <- function (.Object, assayData, phenoData, featureData, 4 exprs = new("matrix"), ...) 5 { 6 if (missing(assayData)) { with .local invoked so as .local(.Object, ...) in the body of initialize. So your 'eset' is the seen as the second argument, and matches by position with the argument 'assayData'; this is not expected to be an ExpressionSet, and trouble ensues. In retrospect the 'right' signature for initialize,ExpressionSet-method would have placed the named arguments after ..., with the user needing to supply named assayData= etc arguments. An additional problem is that the initialize,ExpressionSet-method assumes that .Object is from its prototype, so for instance an exprs with non-zero dimensions is overwritten > eset <- new("ExpressionSet", exprs=matrix(0,10,5)) > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 10 features, 5 samples element names: exprs protocolData: none phenoData: none featureData: none experimentData: use 'experimentData(object)' Annotation: > initialize(eset) ExpressionSet (storageMode: lockedEnvironment) assayData: 0 features, 0 samples element names: exprs protocolData: none phenoData: none featureData: none experimentData: use 'experimentData(object)' Annotation: You're stuck working with the initialize,ExpressionSet-method as defined (changing it now would disrupt a lot of package and user code), probably the easiest way being to write an appropriate initialize method or, probably better given the pitfalls of doing this correctly, write a constructor that does what you want library(Biobase) setClass('A', representation(extraslot='list'), contains='ExpressionSet', prototype=prototype(extraslot=list(a=1:5))) setGeneric("A", function(x, ...) standardGeneric("A")) setMethod(A, "missing", function(x, ...) new("A", ...)) setMethod(A, "ExpressionSet", function(x, ...) { new("A", assayData=assayData(x), phenoData=phenoData(x), featureData=featureData(x), ...) ## protocalData here too? }) ## test eset <- new('ExpressionSet', exprs=matrix(0, 10, 5)) A(eset) A() A(eset)@extraslot A()@extraslot A(eset, extraslot=list(b=5:1))@extraslot A(extraslot=list(b=5:1))@extraslot Martin > > Thank you for any insight on the matter. > Renaud > > sessionInfo: > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_ZA.utf8 LC_NUMERIC=C LC_TIME=en_ZA.utf8 > LC_COLLATE=en_ZA.utf8 LC_MONETARY=C LC_MESSAGES=en_ZA.utf8 > LC_PAPER=en_ZA.utf8 > [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C > LC_MEASUREMENT=en_ZA.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biobase_2.8.0 > > > > > ### > UNIVERSITY OF CAPE TOWN > This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}} > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 6.9 years ago by Martin Morgan ♦♦ 20k
Hi Morgan, thank you very much for the explanation on the initialize method for the class ExpressionSet. I always found the S4 initialization mechanism a bit difficult to handle in the case of inheritance. It often requires to manually pass slots to the parent class, which should be automatic: each class -- developer -- has to deal only with its own data members. Maybe I am too optimistic, but would something like the following definition of initialize,ExpressionSet-method fix the problem without changing the current behaviour for the dependent packages (since I assume they all pass assayData as a first argument): structure(function (.Object, ...) { # check if the first argument is an ExpressionSet # if so: initialize the object with it and tells .local not to # overwrite slots corresponding to missing arguments. # otherwise: s overwrite.missing<- TRUE dotargs<- list(...) if( length(dotargs)> 1&& is(dotargs[[1]], 'ExpressionSet') ){ .Object<- dotargs[[1]] overwrite.missing<- FALSE dotargs<- dotargs[-1] } # .local should initialize (i.e. overwrite) a slot of .Object with its prototype only if overwrite.missing=TRUE, or in any case with the corresponding non missing argument for this slot. .local<- function (.Object, overwrite.missing=TRUE, assayData, phenoData, featureData, exprs = new("matrix"), ...) { if (overwrite.missing&& missing(assayData)) { # stuff ... } # other stuff ... } # call .local with overwrite.missing as its first argument do.call(.local, c(list(.Object, overwrite.missing), dotargs)) } I think this would allow: eset<- new('ExpressionSet', exprs=matrix(0,10,5)) new('ExpressionSet', eset) # simple copy constructor new('ExpressionSet', eset, exprs=matrix(0,20,3)) # overwrite original exprs with the one given in argument # etc... with other slots # and the current behaviour should also work new('ExpressionSet', assayData=assayData(eset), exprs=matrix(0,10,5)) # and initialize will still set the object to its prototype if directly called (which a behaviour one might not want to change as it could be use by other packages) initialize(eset) Thank you. Renaud On 15/12/2010 20:21, Martin Morgan wrote: > On 12/15/2010 09:42 AM, Renaud Gaujoux wrote: >> Hi, >> >> I am trying to extend class ExpressionSet in a very simple way to add an >> extra slot. >> Now suppose I have a valid ExpressionSet object, I want to create an >> object of class 'A' as follows (this always worked with other S4 classes >> I defined): >> >> library(Biobase) >> setClass('A', representation(extraslot='list'), contains='ExpressionSet') >> eset<- new('ExpressionSet') >> new('A', eset) >> >> # this throws the error: >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function >> "annotatedDataFrameFrom", for signature "ExpressionSet" >> #Note: this also does not work with a non-empty ExpressionSet object. >> >> Is this normal? Is there a specific way to extend the class ExpressionSet? >> The classes I found that extend ExpressionSet add an extra element in >> assayData, and from what I saw it requires defining an initialize method >> to pass all the standard parameters to the underlying ExpressionSet >> object (exprs, phenoData, featureData, etc...) > Hi Renaud -- > > This is an unfortunate consequence of the 'initialize' method that your > class inherits from ExpressionSet. 'new' uses the prototype of 'A' to > create .Object, and then passes .Object and other arguments to 'new' > down to 'initialize'. The 'initialize' method inherited from > ExpressionSet is in part > >> head(selectMethod(initialize, 'A')) > 1 structure(function (.Object, ...) > 2 { > 3 .local<- function (.Object, assayData, phenoData, featureData, > 4 exprs = new("matrix"), ...) > 5 { > 6 if (missing(assayData)) { > > with .local invoked so as .local(.Object, ...) in the body of > initialize. So your 'eset' is the seen as the second argument, and > matches by position with the argument 'assayData'; this is not expected > to be an ExpressionSet, and trouble ensues. In retrospect the 'right' > signature for initialize,ExpressionSet-method would have placed the > named arguments after ..., with the user needing to supply named > assayData= etc arguments. > > An additional problem is that the initialize,ExpressionSet-method > assumes that .Object is from its prototype, so for instance an exprs > with non-zero dimensions is overwritten > >> eset<- new("ExpressionSet", exprs=matrix(0,10,5)) >> eset > ExpressionSet (storageMode: lockedEnvironment) > assayData: 10 features, 5 samples > element names: exprs > protocolData: none > phenoData: none > featureData: none > experimentData: use 'experimentData(object)' > Annotation: >> initialize(eset) > ExpressionSet (storageMode: lockedEnvironment) > assayData: 0 features, 0 samples > element names: exprs > protocolData: none > phenoData: none > featureData: none > experimentData: use 'experimentData(object)' > Annotation: > > You're stuck working with the initialize,ExpressionSet-method as defined > (changing it now would disrupt a lot of package and user code), probably > the easiest way being to write an appropriate initialize method or, > probably better given the pitfalls of doing this correctly, write a > constructor that does what you want > > library(Biobase) > setClass('A', representation(extraslot='list'), > contains='ExpressionSet', > prototype=prototype(extraslot=list(a=1:5))) > > setGeneric("A", function(x, ...) standardGeneric("A")) > setMethod(A, "missing", function(x, ...) new("A", ...)) > setMethod(A, "ExpressionSet", function(x, ...) { > new("A", assayData=assayData(x), phenoData=phenoData(x), > featureData=featureData(x), ...) ## protocalData here too? > }) > > ## test > eset<- new('ExpressionSet', exprs=matrix(0, 10, 5)) > A(eset) > A() > A(eset)@extraslot > A()@extraslot > A(eset, extraslot=list(b=5:1))@extraslot > A(extraslot=list(b=5:1))@extraslot > > Martin > >> Thank you for any insight on the matter. >> Renaud >> >> sessionInfo: >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_ZA.utf8 LC_NUMERIC=C LC_TIME=en_ZA.utf8 >> LC_COLLATE=en_ZA.utf8 LC_MONETARY=C LC_MESSAGES=en_ZA.utf8 >> LC_PAPER=en_ZA.utf8 >> [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >> LC_MEASUREMENT=en_ZA.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] Biobase_2.8.0 >> >> >> >> >> ### >> UNIVERSITY OF CAPE TOWN >> This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}} >> >> _______________________________________________ >> 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 > ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}}
ADD REPLYlink written 6.9 years ago by Renaud Gaujoux160
On 12/15/2010 10:05 PM, Renaud Gaujoux wrote: > Hi Morgan, > > thank you very much for the explanation on the initialize method for the > class ExpressionSet. > I always found the S4 initialization mechanism a bit difficult to handle > in the case of inheritance. It often requires to manually pass slots to > the parent class, which should be automatic: each class -- developer -- > has to deal only with its own data members. > > Maybe I am too optimistic, but would something like the following > definition of initialize,ExpressionSet-method fix the problem without > changing the current behaviour for the dependent packages (since I > assume they all pass assayData as a first argument): It's really hard to get S4 right, and the constraints on class and method definition are only weakly enforced, so people have come up with solutions that are not really optimal. From ?initialize, we have ...: data to include in the new object. Named arguments correspond to slots in the class definition. Unnamed arguments must be objects from classes that this class extends. Note the plural 'classes' and setClass("A", representation=representation(a="integer")) setClass("B", representation=representation(b="numeric")) setClass("C", contains=c("A", "B")) > new("C", new("A", a=1:5), new("B", b=pi)) An object of class "C" Slot "a": [1] 1 2 3 4 5 Slot "b": [1] 3.141593 so your solution (checking the first arg) isn't enough. I'll mention that the documentation can point to solutions that will not work well with inheritance, e.g., from ?"initialize-methods" the two examples setMethod("initialize", "traceable", function(.Object, def, tracer, exit, at, print) ... ) and function(.Object, x, ...) { Object <- callNextMethod(.Object, ...) if(!missing(x)) { # do something with x both use arguments that are inconsistent with the description of ?initialize. Also, ExpressionSet was (re)-developed five years ago, and at least some of the more recent classes, e.g., in IRanges, are more appropriately implemented. Martin > > structure(function (.Object, ...) > { > # check if the first argument is an ExpressionSet > # if so: initialize the object with it and tells .local not to > # overwrite slots corresponding to missing arguments. > # otherwise: s > overwrite.missing<- TRUE > dotargs<- list(...) > if( length(dotargs)> 1&& is(dotargs[[1]], 'ExpressionSet') ){ > .Object<- dotargs[[1]] > overwrite.missing<- FALSE > dotargs<- dotargs[-1] > } > > # .local should initialize (i.e. overwrite) a slot of .Object with > its prototype only if overwrite.missing=TRUE, or in any case with the > corresponding non missing argument for this slot. > .local<- function (.Object, overwrite.missing=TRUE, assayData, > phenoData, featureData, > exprs = new("matrix"), ...) > { if (overwrite.missing&& missing(assayData)) { > # stuff ... > } > # other stuff ... > } > > # call .local with overwrite.missing as its first argument > do.call(.local, c(list(.Object, overwrite.missing), dotargs)) > > } > > I think this would allow: > > eset<- new('ExpressionSet', exprs=matrix(0,10,5)) > new('ExpressionSet', eset) # simple copy constructor > new('ExpressionSet', eset, exprs=matrix(0,20,3)) # overwrite original > exprs with the one given in argument > # etc... with other slots > # and the current behaviour should also work > new('ExpressionSet', assayData=assayData(eset), exprs=matrix(0,10,5)) > # and initialize will still set the object to its prototype if directly > called (which a behaviour one might not want to change as it could be > use by other packages) > initialize(eset) > > > Thank you. > Renaud > > > > > > On 15/12/2010 20:21, Martin Morgan wrote: >> On 12/15/2010 09:42 AM, Renaud Gaujoux wrote: >>> Hi, >>> >>> I am trying to extend class ExpressionSet in a very simple way to add an >>> extra slot. >>> Now suppose I have a valid ExpressionSet object, I want to create an >>> object of class 'A' as follows (this always worked with other S4 classes >>> I defined): >>> >>> library(Biobase) >>> setClass('A', representation(extraslot='list'), >>> contains='ExpressionSet') >>> eset<- new('ExpressionSet') >>> new('A', eset) >>> >>> # this throws the error: >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function >>> "annotatedDataFrameFrom", for signature "ExpressionSet" >>> #Note: this also does not work with a non-empty ExpressionSet object. >>> >>> Is this normal? Is there a specific way to extend the class >>> ExpressionSet? >>> The classes I found that extend ExpressionSet add an extra element in >>> assayData, and from what I saw it requires defining an initialize method >>> to pass all the standard parameters to the underlying ExpressionSet >>> object (exprs, phenoData, featureData, etc...) >> Hi Renaud -- >> >> This is an unfortunate consequence of the 'initialize' method that your >> class inherits from ExpressionSet. 'new' uses the prototype of 'A' to >> create .Object, and then passes .Object and other arguments to 'new' >> down to 'initialize'. The 'initialize' method inherited from >> ExpressionSet is in part >> >>> head(selectMethod(initialize, 'A')) >> 1 structure(function (.Object, ...) >> 2 { >> 3 .local<- function (.Object, assayData, phenoData, featureData, >> 4 exprs = new("matrix"), ...) >> 5 { >> 6 if (missing(assayData)) { >> >> with .local invoked so as .local(.Object, ...) in the body of >> initialize. So your 'eset' is the seen as the second argument, and >> matches by position with the argument 'assayData'; this is not expected >> to be an ExpressionSet, and trouble ensues. In retrospect the 'right' >> signature for initialize,ExpressionSet-method would have placed the >> named arguments after ..., with the user needing to supply named >> assayData= etc arguments. >> >> An additional problem is that the initialize,ExpressionSet-method >> assumes that .Object is from its prototype, so for instance an exprs >> with non-zero dimensions is overwritten >> >>> eset<- new("ExpressionSet", exprs=matrix(0,10,5)) >>> eset >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 10 features, 5 samples >> element names: exprs >> protocolData: none >> phenoData: none >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: >>> initialize(eset) >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 0 features, 0 samples >> element names: exprs >> protocolData: none >> phenoData: none >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: >> >> You're stuck working with the initialize,ExpressionSet-method as defined >> (changing it now would disrupt a lot of package and user code), probably >> the easiest way being to write an appropriate initialize method or, >> probably better given the pitfalls of doing this correctly, write a >> constructor that does what you want >> >> library(Biobase) >> setClass('A', representation(extraslot='list'), >> contains='ExpressionSet', >> prototype=prototype(extraslot=list(a=1:5))) >> >> setGeneric("A", function(x, ...) standardGeneric("A")) >> setMethod(A, "missing", function(x, ...) new("A", ...)) >> setMethod(A, "ExpressionSet", function(x, ...) { >> new("A", assayData=assayData(x), phenoData=phenoData(x), >> featureData=featureData(x), ...) ## protocalData here too? >> }) >> >> ## test >> eset<- new('ExpressionSet', exprs=matrix(0, 10, 5)) >> A(eset) >> A() >> A(eset)@extraslot >> A()@extraslot >> A(eset, extraslot=list(b=5:1))@extraslot >> A(extraslot=list(b=5:1))@extraslot >> >> Martin >> >>> Thank you for any insight on the matter. >>> Renaud >>> >>> sessionInfo: >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_ZA.utf8 LC_NUMERIC=C LC_TIME=en_ZA.utf8 >>> LC_COLLATE=en_ZA.utf8 LC_MONETARY=C LC_MESSAGES=en_ZA.utf8 >>> LC_PAPER=en_ZA.utf8 >>> [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >>> LC_MEASUREMENT=en_ZA.utf8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] Biobase_2.8.0 >>> >>> >>> >>> >>> ### >>> UNIVERSITY OF CAPE TOWN >>> This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}} >>> >>> _______________________________________________ >>> 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 >> > > > > ### > UNIVERSITY OF CAPE TOWN > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from > +27 21 650 9111. 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ADD REPLYlink written 6.9 years ago by Martin Morgan ♦♦ 20k
I get your point with the multiple inheritance example, but I did not mean to give a general work around for all inheritance situation, but rather for the specific case of the initialize method of class ExpressionSet. I understand that touching class ExpressionSet is a very sensitive matter given its central role in BioConductor, and it is already great as it is. I will definitely have a look at the IRange class to get some inspirations. Thanks. Renaud On 16/12/2010 08:46, Martin Morgan wrote: > On 12/15/2010 10:05 PM, Renaud Gaujoux wrote: >> Hi Morgan, >> >> thank you very much for the explanation on the initialize method for the >> class ExpressionSet. >> I always found the S4 initialization mechanism a bit difficult to handle >> in the case of inheritance. It often requires to manually pass slots to >> the parent class, which should be automatic: each class -- developer -- >> has to deal only with its own data members. >> >> Maybe I am too optimistic, but would something like the following >> definition of initialize,ExpressionSet-method fix the problem without >> changing the current behaviour for the dependent packages (since I >> assume they all pass assayData as a first argument): > It's really hard to get S4 right, and the constraints on class and > method definition are only weakly enforced, so people have come up with > solutions that are not really optimal. From ?initialize, we have > > ...: data to include in the new object. Named arguments > correspond to slots in the class definition. Unnamed > arguments must be objects from classes that this class > extends. > > Note the plural 'classes' and > > setClass("A", representation=representation(a="integer")) > setClass("B", representation=representation(b="numeric")) > setClass("C", contains=c("A", "B")) > >> new("C", new("A", a=1:5), new("B", b=pi)) > An object of class "C" > Slot "a": > [1] 1 2 3 4 5 > > Slot "b": > [1] 3.141593 > > so your solution (checking the first arg) isn't enough. > > I'll mention that the documentation can point to solutions that will not > work well with inheritance, e.g., from ?"initialize-methods" the two > examples > > setMethod("initialize", "traceable", > function(.Object, def, tracer, exit, at, print) ... > ) > > and > > function(.Object, x, ...) { > Object<- callNextMethod(.Object, ...) > if(!missing(x)) { # do something with x > > both use arguments that are inconsistent with the description of > ?initialize. > > Also, ExpressionSet was (re)-developed five years ago, and at least some > of the more recent classes, e.g., in IRanges, are more appropriately > implemented. > > Martin > >> structure(function (.Object, ...) >> { >> # check if the first argument is an ExpressionSet >> # if so: initialize the object with it and tells .local not to >> # overwrite slots corresponding to missing arguments. >> # otherwise: s >> overwrite.missing<- TRUE >> dotargs<- list(...) >> if( length(dotargs)> 1&& is(dotargs[[1]], 'ExpressionSet') ){ >> .Object<- dotargs[[1]] >> overwrite.missing<- FALSE >> dotargs<- dotargs[-1] >> } >> >> # .local should initialize (i.e. overwrite) a slot of .Object with >> its prototype only if overwrite.missing=TRUE, or in any case with the >> corresponding non missing argument for this slot. >> .local<- function (.Object, overwrite.missing=TRUE, assayData, >> phenoData, featureData, >> exprs = new("matrix"), ...) >> { if (overwrite.missing&& missing(assayData)) { >> # stuff ... >> } >> # other stuff ... >> } >> >> # call .local with overwrite.missing as its first argument >> do.call(.local, c(list(.Object, overwrite.missing), dotargs)) >> >> } >> >> I think this would allow: >> >> eset<- new('ExpressionSet', exprs=matrix(0,10,5)) >> new('ExpressionSet', eset) # simple copy constructor >> new('ExpressionSet', eset, exprs=matrix(0,20,3)) # overwrite original >> exprs with the one given in argument >> # etc... with other slots >> # and the current behaviour should also work >> new('ExpressionSet', assayData=assayData(eset), exprs=matrix(0,10,5)) >> # and initialize will still set the object to its prototype if directly >> called (which a behaviour one might not want to change as it could be >> use by other packages) >> initialize(eset) >> >> >> Thank you. >> Renaud >> >> >> >> >> >> On 15/12/2010 20:21, Martin Morgan wrote: >>> On 12/15/2010 09:42 AM, Renaud Gaujoux wrote: >>>> Hi, >>>> >>>> I am trying to extend class ExpressionSet in a very simple way to add an >>>> extra slot. >>>> Now suppose I have a valid ExpressionSet object, I want to create an >>>> object of class 'A' as follows (this always worked with other S4 classes >>>> I defined): >>>> >>>> library(Biobase) >>>> setClass('A', representation(extraslot='list'), >>>> contains='ExpressionSet') >>>> eset<- new('ExpressionSet') >>>> new('A', eset) >>>> >>>> # this throws the error: >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function >>>> "annotatedDataFrameFrom", for signature "ExpressionSet" >>>> #Note: this also does not work with a non-empty ExpressionSet object. >>>> >>>> Is this normal? Is there a specific way to extend the class >>>> ExpressionSet? >>>> The classes I found that extend ExpressionSet add an extra element in >>>> assayData, and from what I saw it requires defining an initialize method >>>> to pass all the standard parameters to the underlying ExpressionSet >>>> object (exprs, phenoData, featureData, etc...) >>> Hi Renaud -- >>> >>> This is an unfortunate consequence of the 'initialize' method that your >>> class inherits from ExpressionSet. 'new' uses the prototype of 'A' to >>> create .Object, and then passes .Object and other arguments to 'new' >>> down to 'initialize'. The 'initialize' method inherited from >>> ExpressionSet is in part >>> >>>> head(selectMethod(initialize, 'A')) >>> 1 structure(function (.Object, ...) >>> 2 { >>> 3 .local<- function (.Object, assayData, phenoData, featureData, >>> 4 exprs = new("matrix"), ...) >>> 5 { >>> 6 if (missing(assayData)) { >>> >>> with .local invoked so as .local(.Object, ...) in the body of >>> initialize. So your 'eset' is the seen as the second argument, and >>> matches by position with the argument 'assayData'; this is not expected >>> to be an ExpressionSet, and trouble ensues. In retrospect the 'right' >>> signature for initialize,ExpressionSet-method would have placed the >>> named arguments after ..., with the user needing to supply named >>> assayData= etc arguments. >>> >>> An additional problem is that the initialize,ExpressionSet-method >>> assumes that .Object is from its prototype, so for instance an exprs >>> with non-zero dimensions is overwritten >>> >>>> eset<- new("ExpressionSet", exprs=matrix(0,10,5)) >>>> eset >>> ExpressionSet (storageMode: lockedEnvironment) >>> assayData: 10 features, 5 samples >>> element names: exprs >>> protocolData: none >>> phenoData: none >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: >>>> initialize(eset) >>> ExpressionSet (storageMode: lockedEnvironment) >>> assayData: 0 features, 0 samples >>> element names: exprs >>> protocolData: none >>> phenoData: none >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: >>> >>> You're stuck working with the initialize,ExpressionSet-method as defined >>> (changing it now would disrupt a lot of package and user code), probably >>> the easiest way being to write an appropriate initialize method or, >>> probably better given the pitfalls of doing this correctly, write a >>> constructor that does what you want >>> >>> library(Biobase) >>> setClass('A', representation(extraslot='list'), >>> contains='ExpressionSet', >>> prototype=prototype(extraslot=list(a=1:5))) >>> >>> setGeneric("A", function(x, ...) standardGeneric("A")) >>> setMethod(A, "missing", function(x, ...) new("A", ...)) >>> setMethod(A, "ExpressionSet", function(x, ...) { >>> new("A", assayData=assayData(x), phenoData=phenoData(x), >>> featureData=featureData(x), ...) ## protocalData here too? >>> }) >>> >>> ## test >>> eset<- new('ExpressionSet', exprs=matrix(0, 10, 5)) >>> A(eset) >>> A() >>> A(eset)@extraslot >>> A()@extraslot >>> A(eset, extraslot=list(b=5:1))@extraslot >>> A(extraslot=list(b=5:1))@extraslot >>> >>> Martin >>> >>>> Thank you for any insight on the matter. >>>> Renaud >>>> >>>> sessionInfo: >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_ZA.utf8 LC_NUMERIC=C LC_TIME=en_ZA.utf8 >>>> LC_COLLATE=en_ZA.utf8 LC_MONETARY=C LC_MESSAGES=en_ZA.utf8 >>>> LC_PAPER=en_ZA.utf8 >>>> [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >>>> LC_MEASUREMENT=en_ZA.utf8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] Biobase_2.8.0 >>>> >>>> >>>> >>>> >>>> ### >>>> UNIVERSITY OF CAPE TOWN >>>> This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}} >>>> >>>> _______________________________________________ >>>> 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 >> >> >> ### >> UNIVERSITY OF CAPE TOWN >> This e-mail is subject to the UCT ICT policies and e-mail disclaimer >> published on our website at >> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from >> +27 21 650 9111. 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ADD REPLYlink written 6.9 years ago by Renaud Gaujoux160
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