missingPersonIP: Inclusion power for missing person cases

View source: R/missingPersonIP.R

missingPersonIPR Documentation

Inclusion power for missing person cases

Description

Inclusion power for missing person cases

Usage

missingPersonIP(
  reference,
  missing,
  markers,
  nsim = 1,
  threshold = NULL,
  disableMutations = NA,
  seed = NULL,
  verbose = TRUE
)

Arguments

reference

A ped object with attached markers.

missing

The ID label of the missing pedigree member.

markers

A vector indicating the names or indices of markers attached to the source pedigree. If NULL (default), then all markers attached to the source pedigree are used. If alleles or afreq is non-NULL, then this parameter is ignored.

nsim

A positive integer: the number of simulations

threshold

A numeric vector with one or more positive numbers used as the likelihood ratio thresholds for inclusion

disableMutations

This parameter determines how mutation models are treated. Possible values are as follows:

  • NA (the default): Mutations are disabled only for those markers whose known genotypes are consistent with the pedigree. This is determined by temporarily removing all mutation models and checking which markers have nonzero likelihood.

  • TRUE: Mutations are disabled for all markers. This will result in an error if any markers are inconsistent.

  • FALSE: No action is done to disable mutations.

  • A vector containing the names or indices of those markers for which mutations should be disabled.

seed

An integer seed for the random number generator (optional).

verbose

A logical.

Value

A mpIP object, which is essentially a list with the following entries:

  • LRperSim: A numeric vector of length nsim containing the total LR for each simulation.

  • meanLRperMarker: The mean LR per marker, over all simulations.

  • meanLR: The mean total LR over all simulations.

  • meanLogLR: The mean total log10(LR) over all simulations.

  • IP: A named numeric of the same length as threshold. For each element of threshold, the fraction of simulations resulting in a LR exceeding the given number.

  • time: The total computation time.

  • params: A list containing the input parameters missing, markers, nsim, threshold and disableMutations

Examples


# Four siblings; the fourth is missing
x = nuclearPed(4)

# Remaining sibs typed with 5 triallelic markers
x = markerSim(x, N = 5, ids = 3:5, alleles = 1:3, seed = 123, verbose = FALSE)

# Compute exclusion power statistics
missingPersonIP(x, missing = 6, nsim = 5, threshold = c(10, 100))

# Compare with genotypes
x


forrel documentation built on March 18, 2022, 5:19 p.m.