R help - Aug 2011 - Removing funny characters from a column of a data frame

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

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.bansal at 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 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.
>


-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/