Nothing
print.cpg.perm <-
function(x,...) {
cat("\nThe permutation P-values, number of permutations and seed:\n")
print(x$perm.p.values)
cat("\nOther information:\n")
temp<-data.frame(x$info[1,1:4],num.real.Holm=nrow(x$Holm.sig))
if(!is.null(x$FDR.sig)) {
temp<-data.frame(temp,num.real.fdr=nrow(x$FDR.sig))
}
print(temp)
if(nrow(x$results)<10) {
cat("The original analysis:\n")
print(x$results) }
else {
cat("\nThe top ten CpG sites were:\n")
if(sum(order(x$results$P.value)==1:nrow(x$results))==nrow(x$results)) {
print(x$results[1:10,])
}
else {
print(x$results[order(x$results$P.value),][1:10,])
}
cat("\nTo access results for all ", nrow(x$results)," CpG sites use object$results\n",
"or sort(object)$results to obtain results sorted by p-value.\n")
}
cat("\n")
cat(temp$num.real.Holm, "sites were found significant by the Holm method\n")
cat(temp$num.real.fdr, "sites were found significant by", x$info$FDR.method,"method\n")
cat("\nThe beta values were taken from:",as.character(x$info$betainfo),"\n")
stopholder<-which(names(x)=="coefficients")
cat("Other attributes are:",paste(names(x)[1:floor(stopholder/2)],collapse=", "), ",\n",
paste(paste(names(x)[(floor(stopholder/2)+1):stopholder],collapse=", "),".",sep=""),"\nThey can be accessed using the $\n")
invisible(x)
}
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