findRocTpAtFp: Find the ROC true-positive (TP) rate for a given...

In HenrikBengtsson/aroma.cn.eval: Objective Assessment of Copy-Number Estimates

Description

Find the ROC true-positive (TP) rate for a given false-positive (FP) rate.

Usage

## Default S3 method:
findRocTpAtFp(truth, data, fpRate, acc=0.001, recall=NULL, hasNAs=TRUE, isOrdered=FALSE,
  ..., .checkArgs=TRUE, verbose=FALSE)

Arguments

truth	A numeric vector of length N.
data	A numeric vector of length N.
fpRate	A double in [0,1] specifying the target FP rate.
acc	A double specifying the accuracy.
recall	(Optional) Unless truth is given as binary \{0,1\} values, it can be reclassified as such.
hasNAs	If TRUE (FALSE), ROC is calculated as if there are (no) missing values. [Not used!]
isOrdered	If FALSE, data is ordered, otherwise not.
...	Not used.
.checkArgs	If TRUE, arguments are validated, otherwise not.
verbose	See Verbose.

Value

Returns a list with elements:

tpRateEst,tpRateEstRange	The estimated TP rate with lower and upper limits.
fpRateEst,fpRateEstRange	The estimated FP rate with lower and upper limits. This should be close to the request target FP rate.
fpRate	The target FP rate (equals the corresponding argument).
callRate	Fraction of data points called. If less than one, for instance data points with missing values may have been excluded.
orderedIdxs	The indices of the ordered data points corresponding to the lower and upper limits.
w	The weights of the lower and upper limits.

Author(s)

Henrik Bengtsson

See Also

findRocSmoothingForTpAtFp(). scanRocTpAtFp().

Examples

n <- 1000
x <- rnorm(n=n, mean=0, sd=1)
y <- rnorm(n=n, mean=2, sd=1)

T <- integer(2*n)
T[1:n] <- 1L

D <- c(x,y)

fit <- fitRoc(T,D)
par(xaxs="i", yaxs="i")
xlim <- c(0, 0.5)
plot(fit$roc, type="l", lwd=3, xlim=xlim, ylim=c(1-xlim[2], 1))

adj <- c(-0.05,-0.2)
for (fpRate in c(0.2, 0.4)) {
  fit <- findRocTpAtFp(T,D, fpRate=fpRate)
  fp <- fit$fpRateEst
  tp <- fit$tpRateEst
  lines(x=c(0,fp,fp), y=c(tp,tp,xlim[2]))
  text(x=fp, y=xlim[2], sprintf("FP rate: %.3f", fp), srt=90, adj=adj)
  text(x=0, y=tp, sprintf("TP rate: %.3f", tp), adj=adj)
}

HenrikBengtsson/aroma.cn.eval documentation built on Dec. 9, 2019, 12:16 p.m.