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Matrix Question

5 messages · Ben Ganzfried, David Winsemius, Bill Venables

Original
David Winsemius
#
On Jun 2, 2011, at 2:54 PM, Ben Ganzfried wrote:

            

      
      
      
    

        
I haven't quite figured out what your structure really is, and for  
that you should learn to post the output of dput()  on the R object...  
but see if this helps:

 > stg <- c('Stage: T1N0',  'Stage: T2N1', 'Stage: T0N0', 'Stage:  
T1N0', 'Stage: T0N3')
 > Tstg <- sub(".*T(\\d)N.", "\\1", stg)
 > Tstg
#[1] "1" "2" "0" "1" "0"
 > Nstg <- sub(".*T\\dN(\\d)", "\\1", stg)
 > Nstg
#[1] "0" "1" "0" "0" "3"

            

      
      
      
    

        
####----
AND PLEASE DON"T POST THAT CODE WITHOUT A COMMENT.

I noticed it this time, but it is very aggravating to accidentally  
wide out hours of work while trying to offer help.

            

      
      
      
    

        
So here Tstg is tmp

            

      
      
      
    

        
And Nstg is tmp

            

      
      
      
    

        
Just surround it with a pattern and use the ()  , "\\n" mechanism

            

      
      
      
    

        
David Winsemius, MD
West Hartford, CT

  
  


  


      

    

    

      
      

        
      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Bill Venables
    

    

      
      #
    

  


  

      
Here is one way you might do it.

            

      
      
      
    

        
+ characteristics_ch1.3  Stage: T1N0  Stage: T2N1
+ Stage: T0N0  Stage: T1N0  Stage: T0N3
+ ")

            

      
      
      
    

        
Read 11 items

            

      
      
      
    

        
T N
 1 0
 2 1
 0 0
 1 0
 0 3

            

      
      
      
    

        
Now you can print 'out' however you want it, e.g.

            

      
      
      
    

        
This is slightly more complex than it might be as I have allowed for the possibility that your numbers have more than one digit.

Bill Venables. 

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Ben Ganzfried
Sent: Friday, 3 June 2011 4:54 AM
To: r-help at r-project.org
Subject: [R] Matrix Question

Hi,

First of all, I would like to introduce myself as I will probably have many
questions over the next few weeks and want to thank you guys in advance for
your help.  I'm a cancer researcher and I need to learn R to complete a few
projects.  I have an introductory background in Python.

My questions at the moment are based on the following sample input file:
*Sample_Input_File*
 characteristics_ch1.3  Stage: T1N0  Stage: T2N1  Stage: T0N0  Stage:
T1N0  Stage:
T0N3

"characteristics_ch1.3" is a column header in  the input excel file.

"T's" represent stage and "N's" represent degree of disease spreading.

I want to create output that looks like this:
*Sample_Output_File*
T     N
1     0
2     1
0     0
1     0
0     3

As it currently stands, my code is the following:

rm(list=ls())
source("../../functions.R")

uncurated <- read.csv("../uncurated/Sample_Input_File_full_pdata.csv",as.is
=TRUE,row.names=1)

##initial creation of curated dataframe
curated <-
initialCuratedDF(rownames(uncurated),template.filename="Sample_Template_File.csv")

##--------------------
##start the mappings
##--------------------


##title -> alt_sample_name
curated$alt_sample_name <- uncurated$title

#T
tmp <- uncurated$characteristics_ch1.3
tmp <- *??????*
curated$T <- tmp

#N
tmp <- uncurated$characteristics_ch1.3
tmp <- *??????*
curated$N <- tmp

write.table(curated, row.names=FALSE,
file="../curated/Sample_Output_File_curated_pdata.txt",sep="\t")

My question is the following:

What code gets me the desired output (replacing the *??????*'s above)?  I
want to: a) Find the integer value one element to the right of "T"; and b)
find the integer value one element to the right of "N".  I've read the
regular expression tutorial for R, but could only figure out how to grab an
integer value if it is the only integer value in the row (ie more than one
integer value makes this basic regular expression unsuccessful).

Thank you very much for any help you can provide.

Sincerely,

Ben Ganzfried


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