init_pedgene: load Mega2 SQLite database and perform initialization for...

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

load Mega2 SQLite database and perform initialization for pedgene usage

Description

This populates the R data frames from the specified Mega2 SQLite database.

Usage

init_pedgene(db = NULL, verbose = FALSE, traitname = "default", ...)

Arguments

db	specifies the path of a Mega2 SQLite database containing study data.
verbose	TRUE indicates that diagnostic printouts should be enabled. This value is saved in the returned environment.
traitname	Name of the affection status trait to use to set the case/control status; default value = "default".
...	fed to dbmega2_import(); should be bpPosMap= to select from the maps of base pairs, if the default is not desired.

Value

"environment" containing data frames from an SQLite database and some computed values.

Note

init_pedgene calculates schaidPed and pedPer that are used later in the Dopedgene calculation. In addition, it initializes a matrix to aid in translating a genotype allele matrix to a genotype count matrix.

It also initializes the dataframe envir$pedgene_results to zero rows.

See Also

DOpedgene, Mega2pedgene, mkfam

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_pedgene(db, traitname = "default")
ls(ENV)

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