[R] cat bailing out in a for loop

[Uwe Ligges]

Federico Calboli wrote:

> 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?

See ?try.

Uwe Ligges


> Cheers,
> 
> Federico Calboli
>