Jung-Ying Tzeng

PLhap: Penalized-Likelihood Regression for Haplotype Specific Analysis

PLhap implements a penalized regression approach to systematically evaluate the pattern and structure of haplotype effects. The method takes unphased genotype data and outputs the haplotype group structure based on their effect size. PLhap differs from the typical way of haplotype analysis, where haplotype inference focuses on relative effects compared with an arbitrarily chosen baseline haplotype. The typical analysis does not depict the effect structure unless an additional inference procedure is used in a secondary post hoc analysis, and such analysis tends to lack power. By putting an L1 penalty on the pairwise difference of the haplotype effects, PLhap avoids the need to choose a baseline haplotype, and simultaneously carries out effect estimation and effect comparison of all haplotypes. It can serve as a tool to comprehend candidate regions identified from a genome or chromosomal scan.

The methods implemented in this software are described in the following papers.

A Comprehensive Approach to Haplotype Specific Analysis via Penalized Likelihood.  Tzeng and Bondell 2010

General Information

The code is written in R. Notes on using the code are provided in comments in the source file. More detailed instructions will be added to this page soon.

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Main source code for PLhap

Code example illustrating how to run PLhap.

Test data files for PLHap.

myy.bt
myy.qt
myx.adj
mygeno