[R] Iterated Data Input/Output with Random Forests

From: <johnzhou_at_fas.harvard.edu>
Date: Mon 24 Jul 2006 - 02:52:56 EST


Hi,

I am currently writing code to input a few thousand files, run them through the Random Forests package, and then output corresponding results.

When I use the code below:

zz<-textConnection("ex.lm.out", "w")
sink(zz)
tempData<-read.delim(paste("allSnps",1,"Phenotype.phn",sep=""),header=TRUE,sep=",",quote="\"",dec=".") tempData[[1]]<-factor(tempData[[1]])
tempData.rf<-randomForest(tempData[[1]]~.,data=tempData,importance=TRUE,proximity=TRUE,outscale=TRUE,replace=TRUE) tempData.rf
zz<-file(paste("ex",1,".data",sep=""), "w") cat(ex.lm.out, sep="\n", file=zz)
sink()
close(zz)

I am able to successfully input and output for one file. However, if I try to use a for loop or a while statement e.g.

for(i in 1:2)
{
zz<-textConnection("ex.lm.out", "w")
sink(zz)
tempData<-read.delim(paste("allSnps",i,"Phenotype.phn",sep=""),header=TRUE,sep=",",quote="\"",dec=".") tempData[[1]]<-factor(tempData[[1]])
tempData.rf<-randomForest(tempData[[1]]~.,data=tempData,importance=TRUE,proximity=TRUE,outscale=TRUE,replace=TRUE) tempData.rf
zz<-file(paste("ex",i,".data",sep=""), "w") cat(ex.lm.out, sep="\n", file=zz)
sink()
close(zz)
}

I get no error statements but the output is blank. Without the for statement, setting i<-1 works fine.

One other related question is that right now I am trying to gett the loop to work by using the paste() function with a variable (i). However, the paste function returns a string.

If I wanted to make a loop of

tempData$pheno1
tempData$pheno2
tempData$pheno3

...

the paste() function will not work. Is there some other method to achieve the desired effect? Thank you in advance! I have only been working with R for a few days so please bear with my lack of knowledge!

John Zhou



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