mkfam: assemble pedigree information into a data frame

In Mega2R: Accessing and Processing a 'Mega2' Genetic Database

assemble pedigree information into a data frame

Description

Generate a data frame with a row for each person. The observations are:

pedigree	family pedigree name
person	person name
father	father of person
mother	mother of person
sex	sex of person
trait	value of case/control phenotype for person

Usage

mkfam(brkloop = FALSE, traitname = "default", envir = ENV)

Arguments

brkloop	I haven't needed to set this TRUE yet. Maybe never will. If loops are broken, a person will be replaced by a dopple ganger in the same family with a different father/mother. The number of persons per family will be different when there are broken loops. Also, the person_link numbers will be different for all the persons after the first loop is broken.
traitname	Name of the trait to use as case/control value; by default, "default"
envir	An 'environment' that contains all the data frames created from the SQLite database.

Value

data frame that is described above

Note

The columns of this data frame come by selecting the values after merging the data frames: pedigree_table, person_table, and trait_table.

Also, the father and mother columns from person_table are translated from the row index in the person_table to the corresponding name.

This function stores the data frame in the 'environment' and also returns it. The function setfam() stores the data frame into the 'environment' and adjusts the genotype_table and the phenotype_table.

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db)

fam = mkfam()

fam

Mega2R documentation built on May 29, 2024, 1:14 a.m.