Mega2ENVGenABEL: generate gwaa.data-class object

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

generate gwaa.data-class object

Description

create a gwaa.data-class object from the data frames in a Mega2 environment. This function is a front end that eventually calls a C++ Rcpp function that reads the genotype data in Mega2 compressed format and converts it to the GenABEL compressed format. The results of Mega2ENVGenABEL are/should be the same as Mega2GenABEL, but the calculation is much faster, typically a factor of 10 to 20.

Usage

Mega2ENVGenABEL(
  markers = NULL,
  force = TRUE,
  makemap = FALSE,
  sort = TRUE,
  envir = ENV
)

Arguments

markers	data frame of markers to be processed
force	pass value to gwaa conversion function
makemap	pass value to gwaa conversion function
sort	pass value to gwaa conversion function
envir	'environment' containing SQLite database and other globals

Value

gwaa.data-class object created from Mega2R database

Examples

## Not run: 
require("GenABEL")
db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db)
gwaa = Mega2ENVGenABEL(markers=ENV$markers[1:10,])

str(gwaa)
head(summary(gwaa))

## End(Not run)

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