Mega2GenABEL: generate gwaa.data-class object from a *Mega2R* database

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

generate gwaa.data-class object from a Mega2R database

Description

Call the Mega2R functions to: create a .tped file, a .tfam file and a .phe file. Then call the GenABEL functions to process these files: the .tped and the .tfam file are processed by convert.snp.tped to produce a tped.raw file. The latter is combined with a .phe (phenotype) file by load.gwaa.data to create a gwaa.data-class object in memory. All these files are deleted when the exits.

Usage

Mega2GenABEL(markers = NULL, mapno = 0, envir = ENV)

Arguments

markers	data frame of markers to be processed
mapno	specify which map index to use for physical distances
envir	'environment' containing SQLite database and other globals

Value

gwaa.data-class object generated from the Mega2R database

Examples

## Not run: 
require("GenABEL")
db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db)
seqsimgwaa = Mega2GenABEL(markers=ENV$markers[1:10,])

str(seqsimgwaa)
head(summary(seqsimgwaa))

## End(Not run)

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