Mega2R (version 1.1.0)

Mega2GenABEL: 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)

Value

gwaa.data-class object generated from the Mega2R database

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

Examples

if (FALSE) {
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))
}