[R] Matrix Question

[Bill.Venables at csiro.au]

Here is one way you might do it.

> con <- textConnection("
+ characteristics_ch1.3  Stage: T1N0  Stage: T2N1
+ Stage: T0N0  Stage: T1N0  Stage: T0N3
+ ")
> txt <- scan(con, what = "")
Read 11 items
> close(con)
> 
> Ts <- grep("^T", txt, value = TRUE)
> Ts <- sub("T([[:digit:]]+)N([[:digit:]]+)", "\\1x\\2", Ts)
> out <- do.call(rbind, strsplit(Ts, "x"))
> mode(out) <- "numeric"
> dimnames(out) <- list(rep("", nrow(out)), c("T", "N"))
> 
> out
 T N
 1 0
 2 1
 0 0
 1 0
 0 3
> 

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

> sink("outfile.txt")
> out
> sink()

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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