errorRates: errorRates

In breakpointError: Breakpoint detection error

Description

Compute false positive and false negative rates in order to draw ROC curves.

Usage

errorRates(guess.list, break.vec, last.base)

Arguments

guess.list	List of integer vectors, model guesses.
break.vec	Integer vector, breakpoints in true signal.
last.base	Integer scalar, last base in true signal.

Value

data.frame with columns FP, FN, FPR, FNR, TPR.

Author(s)

Toby Dylan Hocking

Examples

seg.size <- 100
means <- c(-3,0,3,0,2,-1,3)/3
mu <- do.call(c,lapply(means,rep,seg.size))
mu.break.after <- which(diff(mu)!=0)

## Choose some bases to sample, and pick them from a normal
## distribution.
base <- as.integer(seq(1,length(mu),l=300))
set.seed(1)
signal <- rnorm(length(base),mu[base],0.5)
profile <- data.frame(base, signal)

library(ggplot2)
ggplot()+
  geom_point(aes(base, signal), data=profile)

library(flsa)
flsa.fit <- flsa(signal, lambda2=10^seq(-2, 2, l=100))
between.vec <- as.integer((base[-1]+base[-length(base)])/2)
flsa.list <- apply(flsa.fit, 1, function(x)between.vec[which(diff(x)!=0)])
flsa.rates <- errorRates(flsa.list, mu.break.after, length(mu))

## Segment that signal with cghseg, and quantify model fit using the
## breakpointError.
result <- run.cghseg(signal, base, maxSegments=15)
cghseg.rates <- errorRates(result$breaks, mu.break.after, length(mu))

rates <-
  rbind(data.frame(cghseg.rates, package="cghseg"),
        data.frame(flsa.rates, package="flsa"))

getMin <- function(df, package, xdiff){
  m <- subset(df, seq_along(error)==which.min(error))
  data.frame(m, package, xdiff)
}
min.err <-
  rbind(getMin(cghseg.rates, "cghseg", -1),
        getMin(flsa.rates, "flsa", 1))

ggplot()+
  ggtitle("ROC curves and minimum breakpointError of two models")+
  scale_y_continuous("True positive rate", limits=c(0, 1))+
  scale_x_continuous("False positive rate")+
  guides(color="none")+
  geom_point(aes(FPR, TPR, color=package),
             data=min.err,
             pch=1)+
  geom_text(aes(FPR+xdiff*0.01, TPR, color=package,
                label=sprintf("FP=%d\nFN=%d\nI=%.1f\n%s",
                  FP, FN, I, package)),
            data=min.err)+
  geom_path(aes(FPR, TPR, group=package, color=package),
            data=rates)

breakpointError documentation built on May 2, 2019, 5:22 p.m.