select.beagle: Select APFA using Beagle

In gRapfa: Acyclic Probabilistic Finite Automata

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	a data frame whose variables are factors. Any missing values are regarded as additional factor levels.
m	is the scale parameter.
b	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

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.

Value

Returns APFA igraph object using Beagle software for the calculations.

Author(s)

Smitha Ankinakatte and David Edwards

See Also

Browning, S., 2006. Multilocus association mapping using variable-length Markov chains. The American Journal of Human Genetics 78 (6), 903-913.

Browning, S., 2008. Missing data imputation and haplotype phase inference for genome wide association studies. Human Genetics 124 (5), 439-450.

Examples

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

gRapfa documentation built on May 2, 2019, 6:54 a.m.