Hi Vikas,
You're overworking yourself here, gsub is vectorized!
df$V5 <- gsub("[^AaCcGgTt\\.,]", "", df$V5)
This will be *substantially* faster than looping (using apply) over
every row of your data frame, since you just care about the 5th column
anyways. Also, I switched your regexp for one that replaces not
AaCcGgTt.,
Cheers,
Josh
On Sun, Aug 7, 2011 at 12:57 PM, Bansal, Vikas <vikas.ban...@kcl.ac.uk> wrote:
> Dear all,
>
> The 5th column of my data frame is like this-
>
> .$.$.$.$.$,$,$...,,,,,.,,.,,...,,,,.,,....,,,T...,,,,,,,,,,,.,,,,,....,,...,,
> ,..,,....,,,,,...,,,..,,......,,,,,,,....,,,.,,,,....,,...G.,,,,,,,,...,,,,,,.,,
> ,t.,,c,,.a.,,,.A,,,,....,,,.....,,,,..........,,,,,..,,,.,,,....,,,,,...,,,$....
> .,,,,..,,,...,,,,,..,,,,,,.............$..,,,,,,...,,..,,$,...,,,,,,,....,,,,,,.
> ,,,,......,,,,.,,.......,.....,,,,,,.,,..,,...,,,,,.,......,.......,,....,,,,..,,
> ,,,,.........,,,,,.....,,,,...,,,.....,,.....,,......,....,,......,.,,..,,,,...,,
> H.,,,..,,.....,,,,..,,,,,,,,,^~.^~.^\".^~.^~.^~.^~,^~,^~,^~,"
>
> I just want to have A,a,C,c,G,g,T,t and dot and comma in the columns.
>
> example of first row should be-
>
> .....,,...,,,,,.,,.,,...,,,,.,,....,,,T...,,,,,,,,,,,.,,,,,....,,...,,
>
>
> currently i am using this code-
>
> df$V5 <- apply(df, 1, function(x)
> gsub("\\:|\\$|\\^|!|\\-|1|2|3|4|5|6|7|8|10|~|H", "",x[5]))
>
> this use of gsub looks odd to me,although result is coming good but I want
> something fast because data is large.I want something like this-
>
> delete everything else except A,a,C,c,G,g,T,t and dot and comma.
>
> Any suggestions Please.
>
>
>
> Thanking you,
> Warm Regards
> Vikas Bansal
> Msc Bioinformatics
> Kings College London
> ______________________________________________
> 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.
>
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
______________________________________________
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.
