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 [[alternative HTML version deleted]]
David Winsemius
2011-Jun-02 19:33 UTC
[R] Regex Question: return digits after particular letters
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 <- tmpSo here Tstg is tmp> > #N > tmp <- uncurated$characteristics_ch1.3 > tmp <- *??????* > curated$N <- tmpAnd 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
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")) > > outT 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 [[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.