LBL.ex2

<p>This dataset consists of affection status, complex sampling weights, a binary stratifying
variable, a binary environmental covariate, and SNP data.</p>

datasets

This function takes a dataset of haplotypes and environmental covariates with one binary phenotype in which rows for individuals of uncertain phase have been augmented by "pseudo-individuals" who carry the possible multilocus genotypes consistent with the single-locus phenotypes. Bayesian lasso is used to find the posterior distributions of logistic regression coefficients, which are then used to calculate Bayes Factor and credible set to test for association with haplotypes, environmental covariates and interactions. The model can handle complex sampling data, in particular, frequency matched cases and controls with controls obtained using stratified sampling. This version can also be applied to a dataset with no environmental covariate and two correlated binary phenotypes.

Xiaochen Yuan

LBLGXE

Logistic Bayesian Lasso for Rare (or Common) Haplotype
Association

LBL.ex2 function

<p>A data frame with variables: <code>affected</code>, <code>wt</code>,
 <code>stra</code>, <code>cov</code>,
 <code>M1.1</code>, <code>M1.2</code>, <code>M2.1</code>, <code>M2.2</code>, <code>M3.1</code>,
 <code>M3.2</code>, <code>M4.1</code>, <code>M4.2</code>, <code>M5.1</code>, <code>M5.2</code>.</p>

Format

This dataset consists of affection status, complex sampling weights, a binary stratifying
variable, a binary environmental covariate, and SNP data. — LBL.ex2

LBL.ex2: This dataset consists of affection status, complex sampling weights, a binary stratifying variable, a binary environmental covariate, and SNP data.

Description

Usage

Arguments

Format