README.md

In andrewparkermorgan/vqtl: An R package for mapping variance-controlling loci (vQTL) in experimental crosses

R/vqtl

This package implements several methods for mapping variance-controlling loci (vQTL) in experimental crosses, whose input and output are compatible with Karl Broman's R/qtl (http://www.rqtl.org/). Also included are functions for producing (static) QTL charts with ggplot2.

Methods implemented

• Double generalized linear model (DGLM) cf. Ronnegard & Valdar 2011 (http://dx.doi.org/10.1534/genetics.111.127068)

TODO: methods to add

• Ridge regression with marker heteroscedasticity (heteroscedastic effects model, HEM) cf. Shen et al. 2013 (http://dx.doi.org/10.1534/genetics.112.146720)
• Ridge regression with linear predictor for variance components (hierarchical generalized linear model, HGLM) using Ronnegard's hglm package (http://cran.r-project.org/web/packages/hglm/)

andrewparkermorgan/vqtl documentation built on May 10, 2019, 11:10 a.m.