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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