HaploCatcher

A Predictive Haplotyping Package

Introduction

This is a public repository for the R package ‘HaploCatcher’. This package utilizes genome-wide molecular data, paired with historical locus/QTL/gene information, to train machine learning algorithms to produce predictive haplotype calls for lines which are genotyped with high density molecular platforms, yet not genotyped for the specific locus/QTL/gene in question. Any questions related to development, maintenance, and potential errors can be directed here.

Installation

To install HaploCatcher in R, users can use the following function taken from the devtools package:

# Install HaploCatcher
devtools::install_github("zjwinn/HaploCatcher")

It is recommended to install using the above code to get the most up-to-date version of HaploCatcher. To install from CRAN instead, use the following code in R:

# Install HaploCatcher from CRAN
install.packages("HaploCatcher")

Getting Started

To understand all necessary inputs for HaploCatcher, users can follow the tutorial laid out in the following R vignette titled, “An Intro to HaploCatcher.” To call on the vignette directly from the R terminal, use the following R code after installing HaploCatcher:

# Call vignette
vignette("An_Intro_to_HaploCatcher")

News

See the release notes for a full history of changes. The current release, HaploCatcher 2.0.1, is a major restructure for speed and maintainability that also adds user-definable case labels (het_label / neg_label) so you are no longer locked into the gene / het_gene / non_gene naming convention.