[R] R regular expression to extract words with the query string.
Hi, Is there a way in R to get the string which matches the expression, where the expression is a substring of the parent string. Lets say, I have $i - transcript:ENST112334 pid:ENSP12345 What I need is the string pid:ENSP12345 from $i using the query ENSP. Appreciate your comments. Praveen Surendran School of Medicine and Medical Sciences University College Dublin Belfiled, Dublin 4 Ireland. [[alternative HTML version deleted]] __ 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.
Re: [R] R regular expression to extract words with the query string.
Try this: sapply(strsplit(i, ' '), grep, pattern='ENSP', value = T) On Wed, Jul 8, 2009 at 10:04 AM, Praveen Surendran praveen.surend...@ucd.ie wrote: Hi, Is there a way in R to get the string which matches the expression, where the expression is a substring of the parent string. Lets say, I have $i - transcript:ENST112334 pid:ENSP12345 What I need is the string pid:ENSP12345 from $i using the query ENSP. Appreciate your comments. Praveen Surendran School of Medicine and Medical Sciences University College Dublin Belfiled, Dublin 4 Ireland. [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ 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.
[R] R regular expression to extract words with the query string.
Thanks Henrique. This is indeed short and quite simple compared to what I was using which goes like... unlist(strsplit(i,split= ))[grep(ENSP,unlist(strsplit(i,split= )))] J Cheers, Praveen. From: Henrique Dallazuanna [mailto:www...@gmail.com] Sent: 08 July 2009 14:18 To: praveen.surend...@ucd.ie Cc: r-help@r-project.org Subject: Re: [R] R regular expression to extract words with the query string. Try this: sapply(strsplit(i, ' '), grep, pattern='ENSP', value = T) On Wed, Jul 8, 2009 at 10:04 AM, Praveen Surendran praveen.surend...@ucd.ie wrote: Hi, Is there a way in R to get the string which matches the expression, where the expression is a substring of the parent string. Lets say, I have $i - transcript:ENST112334 pid:ENSP12345 What I need is the string pid:ENSP12345 from $i using the query ENSP. Appreciate your comments. Praveen Surendran School of Medicine and Medical Sciences University College Dublin Belfiled, Dublin 4 Ireland. [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ 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.
Re: [R] R regular expression to extract words with the query string.
Dear Praveen, Try also: strsplit(i,' ')[[1]][2] # [1] pid:ENSP12345 HTH, Jorge On Wed, Jul 8, 2009 at 9:04 AM, Praveen Surendran praveen.surend...@ucd.iewrote: Hi, Is there a way in R to get the string which matches the expression, where the expression is a substring of the parent string. Lets say, I have $i - transcript:ENST112334 pid:ENSP12345 What I need is the string pid:ENSP12345 from $i using the query ENSP. Appreciate your comments. Praveen Surendran School of Medicine and Medical Sciences University College Dublin Belfiled, Dublin 4 Ireland. [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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.
Re: [R] R regular expression to extract words with the query string.
Try this: library(gsubfn) i - transcript:ENST112334 pid:ENSP12345 strapply(i, paste(\\w*, ENSP, \\w*, sep = ), c, simplify = unlist) This says to match any number (possibly zero) of word characters followed by ENSP followed by more word characters. c just returns the match without further processing and unlist unlists the result giving a character vector (which otherwise would be a list). See http://gsubfn.googlecode.com for more info. On Wed, Jul 8, 2009 at 9:04 AM, Praveen Surendranpraveen.surend...@ucd.ie wrote: Hi, Is there a way in R to get the string which matches the expression, where the expression is a substring of the parent string. Lets say, I have $i - transcript:ENST112334 pid:ENSP12345 What I need is the string pid:ENSP12345 from $i using the query ENSP. Appreciate your comments. Praveen Surendran School of Medicine and Medical Sciences University College Dublin Belfiled, Dublin 4 Ireland. [[alternative HTML version deleted]] __ 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. __ 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.
Re: [R] R regular expression to extract words with the query string.
The solution below does not include the pid: string before it. This modification works: strapply(i, paste([^ ]*, ENSP, [^ ]*, sep = ), c, simplify = unlist) [1] pid:ENSP12345 On Wed, Jul 8, 2009 at 10:08 AM, Gabor Grothendieckggrothendi...@gmail.com wrote: Try this: library(gsubfn) i - transcript:ENST112334 pid:ENSP12345 strapply(i, paste(\\w*, ENSP, \\w*, sep = ), c, simplify = unlist) This says to match any number (possibly zero) of word characters followed by ENSP followed by more word characters. c just returns the match without further processing and unlist unlists the result giving a character vector (which otherwise would be a list). See http://gsubfn.googlecode.com for more info. On Wed, Jul 8, 2009 at 9:04 AM, Praveen Surendranpraveen.surend...@ucd.ie wrote: Hi, Is there a way in R to get the string which matches the expression, where the expression is a substring of the parent string. Lets say, I have $i - transcript:ENST112334 pid:ENSP12345 What I need is the string pid:ENSP12345 from $i using the query ENSP. Appreciate your comments. Praveen Surendran School of Medicine and Medical Sciences University College Dublin Belfiled, Dublin 4 Ireland. [[alternative HTML version deleted]] __ 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. __ 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.
