dviJoint {dvir}R Documentation

Joint DVI search

Description

This is a redesign of jointDVI(), with narrower scope (no preprocessing steps) and more informative output. The output includes the pairwise GLR matrix based on the joint table.

Usage

dviJoint(
  dvi,
  assignments = NULL,
  ignoreSex = FALSE,
  disableMutations = FALSE,
  maxAssign = 1e+05,
  numCores = 1,
  cutoff = 0,
  verbose = TRUE,
  progress = verbose
)

Arguments

dvi

A dviData object, typically created with dviData().

assignments

A data frame containing the assignments to be considered in the joint analysis. By default, this is automatically generated by taking all combinations from dvi$pairings.

ignoreSex

A logical, only relevant if dvi$pairings is NULL, so that candidate pairings have to be generated.

disableMutations

Either TRUE, FALSE (default) or NA. If NA, mutation modelling is applied only in families where the reference data are incompatible with the pedigree unless at least one mutation has occurred.

maxAssign

A positive integer. If the number of assignments going into the joint calculation exceeds this, the function will abort with an informative error message. Default: 1e5.

numCores

An integer; the number of cores used in parallelisation. Default: 1.

cutoff

A number; if non-negative, the output table is restricted to LRs equal to or exceeding this value.

verbose

A logical.

progress

A logical, indicating if a progress bar should be shown.

Value

A data frame.

Examples

dviJoint(example2)


[Package dvir version 3.3.0 Index]