A Starting Point {bqtl}

Some Introductory Comments

Description

Some pointers to a few key functions in BQTL

New to R?

• Be sure to check out all of the free documentation that comes with R.

• The example function is very helpful in getting familiar with a new function. You type example(fun) and the examples in the documentation for fun are run, then you can read the documentaiton to get a bette sense of what is really going on. My personal favorite is to type par(ask=T), hit the 'enter' key, then example(image), and 'enter' again; after each display you hit the 'enter' key to get to the next one.

• library(bqtl) is needed to load the BQTL functions and data sets.

Key Functions

Data Input

\

make.map.frame

defines the map,

marker.levels

The help page describes several functions that define the coding scheme for marker levels,

make.analysis.obj

combines marker data, phenotype data,and the map.frame to create an object that can be used by data analysis functions.

Maximum Likelihood Methods

\

bqtl

does a host of things from marker regression and interval mapping to full maximum likelihood. The best way to get started is to run example(bqtl) and take a look at the resulting output.

locus

is very helpful in specification of runs.

Approximate Bayesian Analysis

\

linear.bayes

For a good starting point try example(linear.bayes)

Author(s)

Charles C. Berry [e-mail]