
Hi Guys, Both of your ways worked. Thanks a lot for your help! Best,Zhengyu 
 > Date: Wed, 26 Sep 2012 16:28:29 -0700
> From: smartpink111@yahoo.com
> Subject: Re: [R] replace string values with numbers
> To: zhyjiang2006@hotmail.com
> CC: r-help@r-project.org; dwinsemius@comcast.net
> 
> Hi,
> 
> You can also try these:
> 
> Gene<-read.table(text="
> P1 P2 P3
>  CG CG GG
> -- --  AC
>  -- AC CC
> AC  --  AC
> ",header=TRUE,sep="")
> Gene<-sapply(Gene,as.character)
> Gene<-data.frame(gsub("GG","3",Gene))
>  Gene
> #  P1 P2 P3
> #1 CG CG  3
> #2 -- -- AC
> #3 -- AC CC
> #4 AC -- AC
> # str(Gene)
> #'data.frame':    4 obs. of  3 variables:
> # $ P1: Factor w/ 3 levels "--","AC","CG": 3 1 1 2
> #$ P2: Factor w/ 3 levels "--","AC","CG": 3 1 2 1
> # $ P3: Factor w/ 3 levels "3","AC","CC": 1 2 3 2
> 
> 
> #2nd way 
> Gene<-read.table(text="
> P1 P2 P3
>  CG CG GG
> -- --  AC
>  -- AC CC
> AC  --  AC
> ",header=TRUE,sep="")
> 
>  Gene<-within(Gene,{P1<-as.character(P1);P2<-as.character(P2);P3<-as.character(P3)})
> Gene[sapply(Gene,function(x) grepl("GG",x))]<-3
> Gene
>   P1 P2 P3
> #1 CG CG  3
> #2 -- -- AC
> #3 -- AC CC
> #4 AC -- AC
>  str(Gene)
> #'data.frame':    4 obs. of  3 variables:
> # $ P1: chr  "CG" "--" "--" "AC"
> # $ P2: chr  "CG" "--" "AC" "--"
> # $ P3: chr  "3" "AC" "CC" "AC"
> 
> A.K.
> 
> ----- Original Message -----
> From: JiangZhengyu <zhyjiang2006@hotmail.com>
> To: r-help@r-project.org
> Cc: 
> Sent: Wednesday, September 26, 2012 3:52 PM
> Subject: [R] replace string values with numbers
> 
> 
> 
> 
> 
> Hi everyone, I have a data frame Gene with SNPs eg.   P1 P2 P3 
> CG CG GG
> -- --  AC 
> -- AC CC
> AC  --  AC I tried to replace all the GG with a value 3.    Gene[Gene=="GG"]<-3 It always give me:  Warning in `[<-.factor`(`*tmp*`, thisvar, value = 3) :
>   invalid factor level, NAs generated Does any know if there is anything wrong with my code? Thanks, Zhengyu                           
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> 
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