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
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 >
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 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > >