[R] recoding genetic information using gsub

[Martin Morgan]

On 12/5/2014 11:24 AM, Kate Ignatius wrote:
> I have genetic information for several thousand individuals:
>
> A/T
> T/G
> C/G  etc
>
> For some individuals there are some genotypes that are like this:  A/,
> C/, T/, G/ or even just / which represents missing and I want to
> change these to the following:
>
> A/ A/.
> C/ C/.
> G/ G/.
> T/ T/.
> / ./.
> /A ./A
> /C ./C
> /G ./G
> /T ./T
>
> I've tried to use gsub with a command like the following:
>
> gsub("A/","[A/.]", GT[,6])

Hi Kate -- a different approach is to create a 'map' (named character vector) 
describing what you want in terms of what you have; the number of possible 
genotypes is not large.

http://stackoverflow.com/questions/15912210/replace-a-list-of-values-by-another-in-r/15912309#15912309

Martin

>
> but if genotypes arent like the above, the command will change it to
> look something like:
>
> A/.T
> T/.G
> C/.G
>
> Is there anyway to be more specific in gsub?
>
> Thanks!
>
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-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109