[R] FW: how to use by() ?

[Jim Moon]

Thank you for the suggestion, Bill.  The result is not quite what I would like.  Here's sample code for you or anyone else who may be interested:

Al1 = c('A','C','C','C')
Al2 = c('G','G','G','T')
Freq1 = c(0.0078,0.0567,0.9434,0.9908)
MAF = c(0.0078,0.0567,0.0566,0.0092)
m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='')  
m1

Al1 Al2  Freq1    MAF major_allele
1   A   G 0.0078 0.0078            
2   C   G 0.0567 0.0567            
3   C   G 0.9434 0.0566            
4   C   T 0.9908 0.0092            


Using the suggestion involving "with()" (I swapped Al1 and Al2 from before, but this does not affect the nature of the output):

m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al2, Al1));m1

  Al1 Al2  Freq1    MAF major_allele
1   A   G 0.0078 0.0078            1
2   C   G 0.0567 0.0567            1
3   C   G 0.9434 0.0566            2
4   C   T 0.9908 0.0092            2


The output I desire is:
  Al1 Al2  Freq1    MAF major_allele
1   A   G 0.0078 0.0078            G
2   C   G 0.0567 0.0567            G
3   C   G 0.9434 0.0566            C
4   C   T 0.9908 0.0092            C


Jim


-----Original Message-----
From: William Dunlap [mailto:wdunlap at tibco.com] 
Sent: Monday, November 29, 2010 10:02 AM
To: Jim Moon
Subject: RE: [R] how to use by() ?

m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al1, Al2))

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Jim Moon
> Sent: Monday, November 29, 2010 9:44 AM
> To: r-help at r-project.org
> Subject: [R] how to use by() ?
> 
> Hello, All!
> 
> How might one accomplish this using the by() function?
> m1 is a data frame.
> 
> # populate column "m1$major_allele"
> for ( i in 1:length(m1$major_allele)) {
>   if ( m1$Freq1[i] == m1$MAF[i]){
>     m1$major_allele[i] = m1$Al1[i]
>   }
>   else{
>      m1$major_allele[i] = m1$Al2[i]
>   }
> }
> 
> 
> Jim
> 
> 	[[alternative HTML version deleted]]
> 
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