R help - Nov 2010 - Converting Strings to Variable names

Hi all,

I am processing 24 samples data and combine them in single table called
CombinedSamples using following:

CombinedSamples<-rbind(Sample1,Sample2,Sample3)

Now variables Sample1, Sample2 and Sample3 have many different columns.

To make it more flexible for other samples I'm replacing above code with a
for loop:

#Sample is a string vector containing all 24 sample names

for (k in 1:length(Sample))
{
      CombinedSamples<-rbind(get(Sample[k]))
}

This code only stores last sample data as CombinedSample gets overwritten
every time. Using "CombinedSamples[k]" or
"CombinedSamples[k,]" causes
dimension related errors as each Sample has several rows and not just 24. So
how can I assign data of all 24 samples to CombinedSamples?

Thanks,

Anand

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Anand Bambhania wrote:
> Hi all,
> 
> I am processing 24 samples data and combine them in single table called
> CombinedSamples using following:
> 
> CombinedSamples<-rbind(Sample1,Sample2,Sample3)
Please use reproducible examples.
> 
> Now variables Sample1, Sample2 and Sample3 have many different columns.
Then you can't 'rbind' them, correct?

 From ?rbind:

      If there are several matrix arguments, they must all have the same
      number of columns (or rows) and this will be the number of columns
      (or rows) of the result.
> 
> To make it more flexible for other samples I'm replacing above code
with a
> for loop:
> 
> #Sample is a string vector containing all 24 sample names
> 
> for (k in 1:length(Sample))
> {
>       CombinedSamples<-rbind(get(Sample[k]))
> }
> 
> This code only stores last sample data as CombinedSample gets overwritten
> every time. Using "CombinedSamples[k]" or
"CombinedSamples[k,]" causes
> dimension related errors as each Sample has several rows and not just 24.
So
> how can I assign data of all 24 samples to CombinedSamples?
I don't know since I'm unsure of the structure of these objects.

If they all have the same structure, I'd store them in a list and
do:

CombinedSamples <- do.call(rbind, sampleList)

otherwise perhaps using

?Reduce and ?merge.  If you can provide a more complete example
to the list, please do. You need not resort to a for loop/get
hack for this.

Best,
--Erik


> 
> Thanks,
> 
> Anand
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Hi Anand,

Try creating a variable where you can store your data, and append it in your
loop. See added lines of code to include below...

On Thu, Nov 4, 2010 at 9:43 AM, Anand Bambhania
<amb1networks@gmail.com>wrote:
> Hi all,
>
> I am processing 24 samples data and combine them in single table called
> CombinedSamples using following:
>
> CombinedSamples<-rbind(Sample1,Sample2,Sample3)
>
> Now variables Sample1, Sample2 and Sample3 have many different columns.
>
> To make it more flexible for other samples I'm replacing above code
with a
> for loop:
>
> #Sample is a string vector containing all 24 sample names
>
#create a variable to stick your results

res<- NULL
>
> for (k in 1:length(Sample))
> {
>      CombinedSamples<-rbind(get(Sample[k]))
>
      res<-c(res, CombinedSamples)
> }
>
> Now, every iteration of your loop should append CombinedSamples to res, and
you won't overwrite your results every time.

HTH,

Mike


> This code only stores last sample data as CombinedSample gets overwritten
> every time. Using "CombinedSamples[k]" or
"CombinedSamples[k,]" causes
> dimension related errors as each Sample has several rows and not just 24.
> So
> how can I assign data of all 24 samples to CombinedSamples?
>
> Thanks,
>
> Anand
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
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