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README.md

breedTools

R package encapsulating methods presented in Estimation of genome-wide and locus-specific breed composition in pigs published in Translational Animal Science (TAS). Note that functions contained in this package have been tested and used on Linux and Mac platforms only.

breedTools can be used to estimate breed composition from DNA microarray data and has been applied to the estimation of pig breed composition and purity.

The methods in this package require a set of reference data (genotypes).

Table of Contents

  1. Installation
  2. Usage

Installation

NOTE: Several functions in breedTools rely on another package, snpTools. First ensure devtools is installed, then install snpTools with:

devtools::install_github("funkhou9/snpTools")

then install breedTools with:

devtools::install_github("funkhou9/breedTools")

attaching the breedTools package with:

library(breedTools)

will allow access to reference pig datasets.

Usage

Key functions include:

  • solve_composition() to estimate genome-wide breed composition (GWBC) for a set of animals, given a reference panel.

  • solve_KBP() to estimate local, KIT-based breed probabilities (KBP) for a set of animals, based on looking at haplotypes within the KIT region on chromosome 8.

  • screen_purity() combines GWBC and KBP methods and provides a full report for a set of animals.

  • build_KBP() is used to build a new reference panel for KBP estimation. Using this function requires installation of FImpute. Note that the path argument is used to specify the location of the FImpute binary if FImpute is not on your PATH.

  • allele_freq() is used to build a new reference panel for GWBC estimation.

Note other functions in snpTools such as snpTools::filter_geno(), which filters out SNPs based on MAF.

Example GWBC and KBP reference panels GWBC_ref_A, GWBC_ref_B, KBP_ref_A, and KBP_ref_B can be loaded with, for example:

data("GWBC_ref_A")

Note that GWBC_ref_A and KBP_ref_A are used to generate the results in the TAS paper.

About

🐷 Tools designed for the interpretation of breed composition from genomic data

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