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