Nothing
"summary.phylpro" <-
function(object, ...) {
sigSites <- 1
siteWinlocs <- -1
siteChisqs <- -1.0
if (length(object$winlocs)<0) {
cat("\nNo significant Minimum Correlation statistics found.\n\n")
return()
}
siteChisqs[1] <- object$corrs[1];
siteWinlocs[1] <- object$winlocs[1];
pairs <- object$target.seqs[1]
for (i in 2:length(object$winlocs)) {
if(object$winlocs[i] != siteWinlocs[sigSites]) { # found a new site
sigSites <- sigSites+1;
siteChisqs[sigSites]=object$corrs[i];
siteWinlocs[sigSites]=object$winlocs[i];
pairs[sigSites] <- object$target.seqs[i]
}
else {
if(object$corrs[i] < siteChisqs[sigSites]) {
siteChisqs[sigSites] <- object$corrs[i]
pairs[sigSites] <- object$target.seqs[i]
}
else if(object$corrs[i] == siteChisqs[sigSites]) {
# concatenate this pair on end of current list of pairs
pairs[sigSites] <- paste(pairs[sigSites],"\n\t\t\t ", object$target.seqs[i], sep="")
}
} # end of else
} # end of for loop
cat("--------------------------------------------------\n");
cat("There were", sigSites,"site-specific Minimum Correlation statistics significant at the\n");
cat("10 percent level (10th percentile = ", sprintf("%5.3f", object$quants[1]), ", 5th percentile = ",sprintf("%5.3f", object$quants[2]),"):\n\n", sep="");
cat ("Number Location MinCor targets\n")
for (i in 1:length(siteWinlocs)) {
if(siteChisqs[i]<object$quants[1]) star<-"*" else star<-" "
cat(sprintf("%6d %7d %5.3f%s %s\n",i, as.integer(siteWinlocs[i]), siteChisqs[i], star, pairs[i]));
}
cat("--------------------------------------------------\n");
cat("Notes - \"Location\" is the polymorphic site just before the proposed breakpoint.\n");
cat(" - MinCor statistics significant at the 5 percent level indicated by a * \n\n");
a <- list(siteWinlocs = siteWinlocs, siteChisqs = siteChisqs, pairs = pairs)
invisible(a)
}
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