dbmega2_import {Mega2R}

read Mega2 SQLite database into R

Description

Read the fields of SQLite data base tables that are required for Mega2R into data frames. These data frames are stored in an 'environment' which is returned. This function also adds some state data, extra data frames, and computed data frames to the 'environment'.

Usage

dbmega2_import(dbname,
               bpPosMap = NULL,
               verbose = FALSE)

Arguments

dbname

file path to SQLite database.

bpPosMap

index that specifies which map in the map_table should be used for marker chromosome/position. If it is NULL, the internal variable base_pair_position_index is used instead. showMapNames() shows the association between map name and map number.

verbose

print out statistics on the name/size of each table read and show column headers. Also, save the verbose value for use by other Mega2R functions.

Value

envir an environment that contains all the data frames made from the SQLite database.

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = dbmega2_import(db, verbose = TRUE)

ENV = dbmega2_import(db)