errorRate {relSim}

Returns the false positive or false negative rates for a set of IBS and/or KI thresholds

Description

This function is used to calcalate the various tables in the work of Ge et al. and Balding et al. Specifically it can be used to calculate the false positive rate for unrelated pairs being identified as full-sibs or parent-child pairs under differing levels of IBS or KI (or both) thresholds. It can also be used to calculate the false negative rates for full-sib, or parent-child, pairs being identified as unrelated, again with differing levels of IBS, KI or both.

Usage

errorRate(
  simResults,
  bIBS = TRUE,
  bKI = FALSE,
  rel = "UN",
  IBSthresh = 14:17,
  KIthresh = c(1000, 10000, 1e+05, 1e+06),
  nLoci = 13
)

Arguments

simResults

A data.frame with three columns labelled sib, pc and ibs. This will usually be obtained from a call to sim or readResults.

bIBS

If TRUE then IBS thresholds are used to generate the error rates. If both bIBS and bKI are TRUE then both criteria are used.

bKI

If TRUE then KI thresholds are used to generate the error rates. If both bIBS and bKI are TRUE then both criteria are used.

rel

The relationship used in the simulation. Must be one of 'UN', 'FS' or 'PC'.

IBSthresh

A vector of IBS values that can be used to classify the results as being related (or not).

KIthresh

A vector of KI threshold values that can be used to classify the results as being related (or not).

nLoci

The number of loci being used in the multiplex. This dictates the upper bound on the IBS values.

Value

A vector (or a two-column matrix) of false negative or false positive rates. If the relationship is 'UN' then false positive rates are returned for parent-child and full-sibs, with parent-child being in column 1 and full-sibs in column 2. If the relationship is 'PC' then the false negative rate is returned for parent-child pairs, and if it is 'FS' then the false negative rate for full-sibs.

Author(s)

James M. Curran

See Also

sim, readResults

Examples

## not run
## Not run: data(fbiCaucs)
unrel = sim(10000)
errorRate(unrel)

## End(Not run)