Nothing
`print.simAutoCross` <-
function(x, ..., row.index=c(1:min(10,nrow(x$markers))),
col.index=c(1:min(10,ncol(x$markers)))){
## Description: print object of class simAutoCross
## Arguments:
## x: object of class simAutoCross
## row.index: which rows to print
## col.index: which columns to print
cat("Autopolyploid dominant markers for crosses generated at",
x$time.generated, "\nwith call:\n")
print(x$call)
cat("\nPloidy level is:",x$ploidy.level,"(", x$p01$E.segRatio$ploidy.name,")\n")
cat("The proportion of markers of each parental type were\n")
print(x$prop.par.type)
cat("Theoretical segregation proportions:\n")
cat("p10:\n"); print(unlist(x[["p10"]]$E.segRatio))
cat("p01:\n"); print(unlist(x[["p01"]]$E.segRatio))
cat("p11:\n"); print(unlist(x[["p11"]]$E.segRatio))
cat("\nProportions in each dosage class:\n")
cat("p10:\n"); print(unlist(x[["p10"]]$dose.proportion))
cat("p01:\n"); print(unlist(x[["p01"]]$dose.proportion))
cat("p11:\n"); print(unlist(x[["p11"]]$dose.proportion))
cat("No. of markers generated from multinomial distribution:\n")
cat("p10:\n"); print(x[["p10"]]$true.doses$table.doses)
cat("p01:\n"); print(x[["p01"]]$true.doses$table.doses)
cat("p11:\n"); print(x[["p11"]]$true.doses$table.doses)
cat("\nOverall: data were generated for",x$n.individuals,"individuals with",
x$n.markers,"markers\nA subset is:\n")
print(cbind(x$markers[row.index,col.index],
cbind(r=x$seg.ratios$r[row.index], n=x$seg.ratios$n[row.index],
ratio=x$seg.ratios$seg.ratio[row.index],
dose=x$name.true.dose[row.index])),
quote=FALSE, justify="right-justified", ...)
## print(x$markers[row.index,col.index])
## if misclassified
if (length(x$misclass.info$proportion) != 0) {
if (x$misclass.info$proportion != 0) {
cat("Marker data were misclassified for",100*x$misclass.info$proportion,
"% offspring markers at random\n")
}
}
if (length(x$parent.misclass.info$proportion) != 0) {
if (x$parent.misclass.info$proportion != 0) {
cat("Marker data were misclassified for",100*x$parent.misclass.info$proportion,
"% parental markers at random\n")
}
}
## if bands missed
if (length(x$misclass.info$bands.proportion) != 0) {
if (x$misclass.info$bands.proportion != 0) {
cat("Dominant marker bands were set missing for",
100*x$misclass.info$bands.proportion,
"% offspring markers at random\n")
}
}
if (length(x$parent.misclass.info$bands.proportion) != 0) {
if (x$parent.misclass.info$bands.proportion != 0) {
cat("Dominant marker bands were set missing for",
100*x$parent.misclass.info$bands.proportion, "% parental markers at random\n")
}
}
## if missing values
if (length(x$na.proportion) != 0) {
if (mode(x$na.proportion$na.proportion) == "numeric") {
if (x$na.proportion$na.proportion != 0) {
cat("Missing data generated for",100*x$na.proportion$na.proportion,
"% offspring markers at random\n")
}
} else {
if (mode(x$na.proportion$na.proportion) == "list") {
cat("Missing values generated for:\n")
cat("Markers:",100*x$na.proportion$na.proportion$marker[1],
"% offspring markers had",
100*x$na.proportion$na.proportion$marker[2],"missing at random\n")
cat("Individuals:",100*x$na.proportion$na.proportion$indiv[1],
"% offspring individuals had",
100*x$na.proportion$na.proportion$indiv[2],"missing at random\n")
}
}
}
}
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