evaluating a character string as a variable name in an ExpressionSet object
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@kavitha-venkatesan-3399
Last seen 7.5 years ago
United States
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$score in turn. Furthermore, I need to be able to generalize my code so that I can retrieve this factor for any phenodata variable in any given ExpressionSet object. Clearly I cannot do something like for (i in c(1:length(varLabels(sample.ExpressionSet))) { class_label <- varLabels(sample.ExpresionSet)[i] class_label_factor <- sample.ExpressionSet$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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@sean-davis-490
Last seen 6 weeks ago
United States
On Thu, Apr 16, 2009 at 5:58 PM, Kavitha Venkatesan < kavitha.venkatesan@gmail.com> wrote: > 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$score in turn. > Furthermore, I need to be able to generalize my code so that I can retrieve > this factor for any phenodata variable in any given ExpressionSet object. > > Clearly I cannot do something like > > for (i in c(1:length(varLabels(sample.ExpressionSet))) > { > class_label <- varLabels(sample.ExpresionSet)[i] > class_label_factor <- sample.ExpressionSet$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! > If i is your class label: pData(sample.ExpressionSet)[,i] does that do what you need? Sean [[alternative HTML version deleted]]
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@saroj-mohapatra-1446
Last seen 8.1 years ago
Hi Kavitha: Are you looking for something like this: > ls() character(0) > # I have a string called "reallyfunnyvariable" > mystr = "reallyfunnyvariable" # I want to convert this to a variable with the same name; I want it to be a list eval(parse(text=paste(mystr,"=list()",sep=""))) # Now I have the variable > ls() [1] "mystr" "reallyfunnyvariable" # it is a list > reallyfunnyvariable list() You have to be careful though while turning strings into variable, especially in the "batch" mode - what if the string is something like "plot"? You might want to add a clause for first checking if the variable exists, before assigning the variable name. Best, Saroj ----- Original Message ----- From: "Kavitha Venkatesan" <kavitha.venkatesan@gmail.com> To: bioconductor at stat.math.ethz.ch Sent: Thursday, April 16, 2009 5:58:44 PM GMT -05:00 US/Canada Eastern Subject: [BioC] evaluating a character string as a variable name in an ExpressionSet object 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$score in turn. Furthermore, I need to be able to generalize my code so that I can retrieve this factor for any phenodata variable in any given ExpressionSet object. Clearly I cannot do something like for (i in c(1:length(varLabels(sample.ExpressionSet))) { class_label <- varLabels(sample.ExpresionSet)[i] class_label_factor <- sample.ExpressionSet$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]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology VBI @ Virginia Tech
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