validate_trio_consistency {networkR}

Validate pedigree trio information consistency

Description

Simple tests to chech the consistency of the pedigree trio family data. Currently the following checks are undertaken: 1) that no duplicates ids are found; 2) that the primary id is not missing for anyone; 3) that founders have both the father and mother id missing; 4) that individuals are not both classified as male (fathers and mothers);

Usage

validate_trio_consistency(id, fid, mid, sex = NULL)

Arguments

id

Numeric. The id of the individual. These values should be unique

fid

Numeric. The father id. NA or 0 are used for missing.

mid

Numeric. The mother id. NA or 0 are used for missing.

sex

An optional numeric vector with the sex of the individual. Only four values should be present 1 (male), 2 (female), 0 or NA (missing)

Details

There are no checks of persons being both mother and father, nor being its own parent and incest checks are not performed. In other words, the obj is assumed to be sane, but possibly immoral.

Value

Throws an error if an inconsistency is found. Otherwise returns TRUE.

Author(s)

Claus Thorn Ekstrøm, [e-mail]

Examples

library("data.table")
id <- 1:12
fid <- c(NA,  0, 1, 1, NA, 23, 45, 5, 5, 7, 10, 10)
mid <- c(NA, NA, 2, 2,  0, 56, 46, 6, 6, 6, 9, 11)

validate_trio_consistency(id, fid, mid)