On Jun 2, 2011, at 2:54 PM, Ben Ganzfried wrote:
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
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"
"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())
####----
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.
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
So here Tstg is tmp
#N
tmp <- uncurated$characteristics_ch1.3
tmp <- *??????*
curated$N <- tmp
And Nstg is 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).
Just surround it with a pattern and use the () , "\\n" mechanism
Thank you very much for any help you can provide.
Sincerely,
Ben Ganzfried
[[alternative HTML version deleted]]
David Winsemius, MD
West Hartford, CT
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