For example, DF will usually have numerous columns with sample1.at sample1.dp sample1.fg sample2.at sample2.dp sample2.fg and so on....
I'm running this code in R as part of a shell script which runs over several different file sizes so sometimes it will come across a file with one sample in it: i.e. sample1: when the R code runs through this file... trying to grep out the "sample1.at" column does not work and it will halt and stop. Here is some sample data... say I want to get out the AT_ only column.... Sample_1 AT_1 A/A RR G/G AA T/T AA G/A RA G/G RR C/C AA C/C AA C/T RA A/A AA T/G RA it will have a problem grepping out this single column. On Tue, Oct 14, 2014 at 10:38 AM, John McKown <john.archie.mck...@gmail.com> wrote: > On Tue, Oct 14, 2014 at 9:23 AM, Kate Ignatius <kate.ignat...@gmail.com> > wrote: >> I'm having an issue with grep: >> >> I have numerous columns that end with .at... when I use grep like so: >> >> df[,grep(".at",colnames(df))] >> >> it works fine. When I have one column that ends with .at, it does not >> work. Why is that? As this is loop with varying number of columns >> ending in .at I would like some code that would work with 1 to n >> number of columns. >> >> Is there something more optimal than grep? >> >> Thanks! > > I can't answer your direct question. But do you realize that your code > does not match your words? The grep show does not _only_ match columns > who name end with the characters '.at'. It matches all column names > which contain any character followed by the characters "at". To do the > match with only columns whose names end with the characters ".at", you > need: grep("\.at$",colnames(df)). > > You might want to post an example which fails. Just to be complete, be > sure to use the dput() function so that it is easy for members of the > group to cut'n'paste to get your data into our own R workspace. > > -- > There is nothing more pleasant than traveling and meeting new people! > Genghis Khan > > Maranatha! <>< > John McKown ______________________________________________ R-help@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.