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
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