Nothing
print.compareSNPs <- function(x,...)
{
if (attr(x,"groups"))
cat("*********** Summary of genetic data (SNPs) by groups ***********\n")
else
cat("*********** Summary of genetic data (SNPs) ***********\n")
if (attr(x,"groups")){
for (i in 1:length(x)){
if (i < length(x)){
x.i<-x[[i]]
x.i$A1<-ifelse(is.na(x.i$A1),"-",x.i$A1)
x.i$A2<-ifelse(is.na(x.i$A2),"-",x.i$A2)
x.i$Hom1.p<-ifelse(is.na(x.i$Hom1.p),0,x.i$Hom1.p)
x.i$Het.p<-ifelse(is.na(x.i$Het.p),0,x.i$Het.p)
x.i$Hom2.p<-ifelse(is.na(x.i$Hom2.p),0,x.i$Hom2.p)
temp<-data.frame(SNP=x.i$SNP,
Ntyped=x.i$Ntyped,
MAF=paste(format2(x.i[,"MAF"]*100,1),"%",sep=""),
Genotypes=I(with(x.i,apply(cbind(paste(A1,A1,sep=""),paste(A1,A2,sep=""),paste(A2,A2,sep="")),1,paste,collapse="|"))),
Genotypes.p=with(x.i,apply(cbind(format(format2(Hom1.p*100,1),justify="right"),format(format2(Het.p*100,1),justify="right"),format(format2(Hom2.p*100,1),justify="right")),1,paste,collapse="|")),
HWE.p=format2(x.i[,"HWE.p"],3))
temp$Genotypes<-ifelse(x.i$A1=='-' & x.i$A2=='-','-',
ifelse(x.i$A2=='-',apply(cbind(x.i$A1,x.i$A1),1,paste,collapse=""),temp$Genotypes))
}else{
temp<-x[[i]]
names(temp)[2]<-"p.value"
temp[,"p.value"] <- format2(temp[,"p.value"],3)
}
cat("\n\n ***",names(x)[i],"***\n\n")
printTable(temp)
}
} else {
x$A1<-ifelse(is.na(x$A1),"-",x$A1)
x$A2<-ifelse(is.na(x$A2),"-",x$A2)
x$Hom1.p<-ifelse(is.na(x$Hom1.p),0,x$Hom1.p)
x$Het.p<-ifelse(is.na(x$Het.p),0,x$Het.p)
x$Hom2.p<-ifelse(is.na(x$Hom2.p),0,x$Hom2.p)
temp<-data.frame(SNP=x$SNP,
Ntyped=x$Ntyped,
MAF=paste(format2(x[,"MAF"]*100,1),"%",sep=""),
Genotypes=I(with(x,apply(cbind(paste(A1,A1,sep=""),paste(A1,A2,sep=""),paste(A2,A2,sep="")),1,paste,collapse="|"))),
Genotypes.p=with(x,apply(cbind(format(format2(Hom1.p*100,1),justify="right"),format(format2(Het.p*100,1),justify="right"),format(format2(Hom2.p*100,1),justify="right")),1,paste,collapse="|")),
HWE.p=format2(x[,"HWE.p"],3))
temp$Genotypes<-ifelse(x$A1=='-' & x$A2=='-','-',
ifelse(x$A2=='-',apply(cbind(x$A1,x$A1),1,paste,collapse=""),temp$Genotypes))
printTable(temp)
}
}
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