select.beagle: Select APFA using Beagle

Description

select.beagle runs Beagle software selection method to build APFA model.

Usage

select.beagle(A, m=4, b=0.2, dir = '', row.marker = FALSE, col.hap = FALSE)

Arguments

a data frame whose variables are factors. Any missing values are regarded as additional factor levels.

is the scale parameter.

the shift parameter

dir

path of the directory to find the beagle.jar file. The destined path should end with either '\' or '//'. If dir='', by default the function considers the beagle.jar is in the same directory as R is running.

row.marker

For genotype data, to spcify whether the markers are in rows or columns

col.hap

For genotype data, to specify whether the haplotypes are in rows or in columns

Value

Returns APFA igraph object using Beagle software for the calculations.

Details

select.beagle is an interface in R to work with Beagle software. Beagle is a software package for analysis of large scale genetic data sets. Beagle is written in Java, hence the Java interpreter needs to needs to be installed. More details on downloading and installing Beagle can be found in http://faculty.washington.edu/browning/beagle/beagle.html.

Examples

Run this code

# you have to have 'beagle.jar' to run the code below,
##library(gRapfa)
##data(Wheeze)
##G <- select.beagle(Wheeze)