read.Mega2DB {Mega2R}

load Mega2 database and initialize family data frame and markers data frame

Description

Call dbmega2_import() with the specified database and create an 'environment', with the SQLite table data loaded into data frames. Also run mkfam() to create the pedigree data frame fam and then store it with setfam(). setfam() modifies the unified_genotype_table (and phenotype_table) to match the family members that remain.

Usage

read.Mega2DB(db, ...)

Arguments

db

specify SQLite database to load

...

additional arguments to pass to dbmega2_import

Value

an 'environment' that contains all the data frames created from the SQLite database.

Note

By default, mkfam will remove one of each person that was replicated to break loops in the pedigree, see mkfam for details. If you want to leave loops broken, the code is available, but you will have to write your own version of read.Mega2DB with a different invokation of mkfam().

Examples

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