[R] Removing funny characters from a column of a data frame

[Joshua Wiley]

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