[BioC] evaluating a character string as a variable name in an ExpressionSet object

[Martin Morgan]

Kavitha Venkatesan <kavitha.venkatesan at gmail.com> writes:

> Thanks for all your suggestions. Both Martin's suggestions below (simpler
> solution) and Saroj's approach worked.
> FYI- Saroj's approach which when adapted to my situation would entail the
> following code:
>>for(i in varLabels(sample.ExpressionSet))
>> print( eval(parse(text=paste("sample.ExpressionSet","$",i,sep=""))) )

one would not normally do this; it is like making coffee from the
words 'coffee beans' rather than from the coffee beans themselves.

Martin

> Kavitha
>
>
> On Thu, Apr 16, 2009 at 11:41 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
>           Hi Kavitha --     
>
>                Kavitha Venkatesan <kavitha.venkatesan at gmail.com> writes:     
>      > I would like to know how to evaluate a character string as a
>      variable name     > in R. Specifically, I need to "compute" the
>      variable name in the phenoData     > slot of an ExpressionSet
>      object.     >     >> varLabels(sample.ExpressionSet)     > [1] "sex"
>        "type"  "score"     >     > Now I need to retrieve the factors
>      sample.ExpressionSet$sex,     > sample.ExpressionSet$type and
>      sample.ExpressionSet$score in turn.     
>      
>
>
>      Use [[ rather than $.     
>      > data(sample.ExpressionSet)     > sample.ExpressionSet[["sex"]]      [1]
>      Female Male   Male   Male   Female Male   Male   Male   Female Male     [11]
>      Male   Female Male   Male   Female Female Female Male   Male  
>      Female     [21] Male   Female Male   Male   Female Female     Levels:
>      Female Male     
>      e.g.,     
>      > for (lbl in varLabels(sample.ExpressionSet))     +    
>      print(sample.ExpressionSet[[lbl]])      [1] Female Male   Male  
>      Male   Female Male   Male   Male   Female Male     [11] Male  
>      Female Male   Male   Female Female Female Male   Male   Female     [21]
>      Male   Female Male   Male   Female Female     Levels: Female Male      [1]
>      Control Case    Control Case    Case    Control Case    Case    Case     [10]
>      Control Case    Control Case    Case    Case    Control Case  
>       Control     [19] Case    Case    Control Control Control Control
>      Case    Case     Levels: Case Control      [1] 0.75 0.40 0.73 0.42
>      0.93 0.22 0.96 0.79 0.37 0.63 0.26 0.36 0.41 0.80 0.10     [16] 0.41
>      0.16 0.72 0.17 0.74 0.35 0.77 0.27 0.98 0.94 0.32     
>      
>      Martin     
>
>                > Furthermore, I need to be able to generalize my code so
>      that I can retrieve     > this factor for any phenodata variable in
>      any given ExpressionSet object.     >     > Clearly I cannot do
>      something like     >     > for (i in
>      c(1:length(varLabels(sample.ExpressionSet)))     > {     >
>      class_label <- varLabels(sample.ExpresionSet)[i]     >
>      class_label_factor <-  sample.ExpressionSet$class_label     > }     >     >
>      Here class_label is interpreted as a character string by R, but I
>      need for     > it to be evaluated as a variable name. Seems
>      straightforward, but I couldn't     > figure it out...How can I do
>      this? Thanks in advance for any help!     >     > Kavitha     >     
>
>           >       [[alternative HTML version deleted]]     >     >
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>      --     
>
>
>      Martin Morgan     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     
>
>
>

-- 
Martin Morgan
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