findExclusions: Find markers excluding an identification

View source: R/findExclusions.R

findExclusionsR Documentation

Find markers excluding an identification

Description

Find markers for which the genotypes of a candidate individual is incompatible with a pedigree

Usage

findExclusions(x, id, candidate, removeMut = TRUE)

Arguments

x

A ped object or a list of such.

id

A character of length 1; the name of an untyped member of x.

candidate

A singleton pedigree, with genotypes for the same markers as x.

removeMut

A logical. If TRUE (default), all mutations models are stripped.

Value

A character vector containing the names of incompatible markers.

Examples


# Pedigree with 3 siblings; simulate data for first two
x = nuclearPed(3) |>
  setMarkers(locusAttributes = NorwegianFrequencies[1:5]) |>
  profileSim(ids = 3:4, seed = 1)

# Simulate random person
poi = singleton(1) |>
  setMarkers(locusAttributes = NorwegianFrequencies[1:5]) |>
  profileSim(seed = 1)

# Identify incompatible markers
findExclusions(x, id = 5, candidate = poi)   # D21S11

# Inspect
plotPedList(c(x, poi), marker = "D21S11", frames = FALSE)


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