Re: [R] Replacing columns in a data frame using a previous condition

From: Dimitris Rizopoulos <Dimitris.Rizopoulos_at_med.kuleuven.be>
Date: Thu, 14 Feb 2008 21:44:37 +0100

try this:

GERU[6:318] <- lapply(GERU[6:318], function (x) {

     if (length(unique(x[!is.na(x)])) >= 5) x[x == 2] <- 3
     x

})

I hope it helps.

Best,
Dimitris



Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium

Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
      http://www.student.kuleuven.be/~m0390867/dimitris.htm


Quoting Jorge Iván Vélez <jorgeivanvelez_at_gmail.com>:

> Dear R-list,
>
> I'm working with a data frame which dimensions are
>
>> dim(GERU)
> [1] 3468 318
>
> and looks like
>
>> GERU[1:10,1:10]
> ped ind par1 par2 sex sta rs7696470 rs7696470.1 rs1032896 rs1032896.1
> 1 USA5854 2 0 0 2 1 4 4 1 1
> 2 USA5854 3 1 2 1 1 4 4 1 1
> 3 USA5854 4 1 2 2 2 1 4 1 3
> 4 USA5854 5 1 2 1 2 4 2 2 1
> 5 USA5855 1 0 0 1 1 0 0 0 0
> 6 USA5855 2 0 0 2 2 1 0 0 0
> 7 USA5855 3 1 2 1 2 0 2 0 0
> 8 USA5855 4 1 2 1 1 2 0 2 1
> 9 USA5855 5 1 2 1 2 0 1 0 0
> 10 USA5856 1 0 0 1 1 3 3 3 3
>
> What I would like to do is:
>
> 1. Identify which column (from 6 to 318) has more than 4 categories (I
> solved that). In GERU would be rs7696470 and rs7696470.1.
> 2. Using the columns in step 1, replace its entries equals to 2 for 3. For
> example, rs7696470 would be 4,4,1,4,0,1,0,3,0,3 and so on.
> 3. Once replaced the entries, I need to rewrite the columns in GERU.
>
> Here is what I've done:
>
>> # Function to identify columns with 3 or more categories
>> tx=function(x) ifelse(dim(table(x))>4,1,0)
>
>> # Identifying the columns
>> M4=apply(GUPN[,-c(1:6)],2,tx)
>> names(which(MR==1)) # Step 1
> [1] "rs335322" "rs335322.1" "rs186750" "rs186750.1"
> "rs1565901" "rs1565901.1" "rs1565902"
> [8] "rs1565902.1" "rs11131334" "rs11131334.1" "rs1948616" "
> rs1948616.1" "rs4484334" "rs4484334.1"
> [15] "rs1497921" "rs1497921.1" "rs1391320" "rs1391320.1"
> "rs1497913" "rs1497913.1" "rs996208"
> [22] "rs996208.1"
>> # Step 2
>> REPLACE=GUPN[,names(which(AR==1))]
>> RES=apply(REPLACE,2,function(x) ifelse(x==2,3,x))
>> RES[1:10,1:5]
> rs335322 rs335322.1 rs186750 rs186750.1 rs1565901
> 1 1 3 3 3 3
> 2 1 1 3 3 3
> 3 3 3 1 3 3
> 4 1 3 3 3 3
> 5 0 0 0 0 0
> 6 0 0 0 0 0
> 7 0 0 0 0 0
> 8 0 0 0 0 0
> 9 0 0 0 0 0
> 10 1 3 3 3 1
>
> Now, the problem I have is replacing the columns in GERU by the columns in
> RES (step 3). At the end the dimension of the new data set should be
> 3468x318. Any help would be greatly appreciated.
>
> Thanks you so much,
>
>
> Jorge
>
> [[alternative HTML version deleted]]
>
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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. Received on Thu 14 Feb 2008 - 20:48:27 GMT

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