missingPersonEP: Exclusion power for missing person cases

Description Usage Arguments Details Value See Also Examples

View source: R/missingPersonEP.R

Description

This is a special case of exclusionPower() for use in missing person cases. The function computes the probability that a random person is genetically incompatible with the typed relatives of the missing person.

Usage

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missingPersonEP(
  reference,
  missing,
  markers = NULL,
  disableMutations = NA,
  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.

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.

verbose

A logical.

Details

This function is identical to randomPersonEP(), but with different argument names. This makes it consistent with missingPersonIP() and the other 'missing person' functions.

Value

The EPresult object returned by exclusionPower().

See Also

randomPersonEP(), exclusionPower()

Examples

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

# Remaining sibs typed with 4 triallelic markers
x = markerSim(x, N = 4, ids = 3:5, alleles = 1:3, seed = 577, verbose = FALSE)

# Add marker with inconsistency in reference genotypes
# (by default this is ignored by `missingPersonEP()`)
badMarker = marker(x, `3` = 1, `4` = 2, `5` = 3)
x = addMarkers(x, badMarker)

# Compute exclusion power statistics
missingPersonEP(x, missing = 6)

forrel documentation built on March 14, 2021, 1:06 a.m.