RE: [R] cat bailing out in a for loop

From: Liaw, Andy <andy_liaw_at_merck.com>
Date: Wed 06 Apr 2005 - 01:33:59 EST


See ?try.

Andy

> From: Federico Calboli
>
> Dear All,
>
> I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42
> SNPs. I am using the function HWE.exact from the package "genetics".
>
> In order not to do a lot of coding "by hand", I have a for loop that
> goes through each column (each column is one SNP) and gives me the
> p.value for HWE.exact. Unfortunately some SNP have reached
> fixation and
> HWE.exact requires a 2 alleles scenario.
>
> So my problem is that my for loop:
>
> ##################################################
>
> for (i in 1:42){
> xxx<-HWE.exact(genotype(laba.con[,i+3], sep=""))
> cat(colnames(laba)[i+3],xxx$p.value,"\n")}
>
> ##################################################
>
> bails out as soon as it hits a SNP at fixation for one allele, because
> HWE.exact fails.
>
> I have a lot of this game to play and checking things by hand is not
> idea, and I do not care about failed SNP, all I want is for
> the loop to
> carry on regardless of what's in xxx$p.value, even if HWE.exact failed
> to calculte it. Dump anything in there!
>
> Is there any way of forcing the loop to carry on?
>
> Cheers,
>
> Federico Calboli
>
> --
> Federico C. F. Calboli
> Department of Epidemiology and Public Health
> Imperial College, St Mary's Campus
> Norfolk Place, London W2 1PG
>
> Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
>
> f.calboli [.a.t] imperial.ac.uk
> f.calboli [.a.t] gmail.com
>
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>
>



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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 Received on Wed Apr 06 01:50:05 2005

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