Entering edit mode
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
