familias2dvir: Convert a Familias file to DVI data

Description

This is a wrapper for pedFamilias::readFam() that reads Familias files with DVI information.

Usage

familias2dvir(
  famfile,
  victimPrefix = NULL,
  familyPrefix = NULL,
  refPrefix = NULL,
  missingPrefix = NULL,
  missingFormat = NULL,
  othersPrefix = NULL,
  verbose = FALSE,
  missingIdentifier = "^Missing"
)

Value

A dviData object.

Arguments

famfile

Path to Familias file.

victimPrefix

Prefix used to label PM individuals.

familyPrefix

Prefix used to label the AM families.

refPrefix

Prefix used to label the reference individuals, i.e., the typed members of the AM families.

missingPrefix

Prefix used to label the missing persons. At most one of missingPrefix and missingFormat can be given.

missingFormat

A string indicating family-wise labelling of missing persons, using [FAM], [IDX], [MIS] as place holders with the following meanings (see Examples):

[FAM]: family index
[IDX]: index of missing person within the family
[MIS]: index within all missing persons

othersPrefix

Prefix used to label other untyped individuals. Use "" for numeric labels ( 1, 2, ...).

verbose

A logical, passed on to readFam().

missingIdentifier

A character of length 1 used to identify missing persons in the Familias file. The default chooses everyone whose label begins with "Missing".

Details

The sex of the missing persons need to be checked as this information may not be correctly recorded in the fam file.

Examples

Run this code


# Family with three missing
file = system.file("extdata", "dvi-example.fam", package="dvir")

# Read file without relabelling
y = familias2dvir(file)
plotDVI(y)

# With relabelling
z = familias2dvir(file, missingFormat = "M[FAM]-[IDX]",
                   refPrefix = "ref", othersPrefix = "E")
plotDVI(z)