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

[David Winsemius]

On Nov 29, 2010, at 1:36 PM, Jim Moon wrote:

> 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

I suspect that you have just been bitten by the data.frame- 
stringsAsFactors=TRUE crocodile. Since you are comparing floating  
point numbers, you are also wading in rivers where floating-point  
crocodiles are also hungry and searching out their next victim.

-- 
David.


> 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]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> 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.
>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.

David Winsemius, MD
West Hartford, CT