Pig: A dataset contains an example of MSUPRP F2 Pig data

In chenchunyu88/BATools: BATools: An R package that extends 'Bayesian Alphabet' for Whole Genome Prediction and Genome-wide association study

Description

A dataset containing the MSUPRP example dataset with 176 pig with 20597 SNPs have both genotype and phenotype infomation. The example data is a subset of MSUPRP (Gualdron Duarte et al. 2014). The phenotype used in the example is drip loss in pork.

Usage

data(Pig)

Format

• PigPheno data.frame of the phenotypes

• PigM matrix of SNP marker genotypes coded as 0,1,2

• PigMap data.frame containing chromosome, postition and window for SNPs in PigM

• PigPed data.frame of pedigree of the pig population

• PigAlleleFreq allele frequency of F0

• PigAinv matrix of the inverse of the additive relationship matrix based on Pig pedigree

• PigA matrix of the additive relationship matrix based on Pig pedigree

Source

https://github.com/steibelj/gwaR/blob/master/data/MSUPRP_sample.RData

How the data is prepared for BATools: https://github.com/chenchunyu88/batoolsdata/blob/master/MSUPRP.ipynb

References

Jose L Gualdron Duarte, Rodolfo JC Cantet, Ronald O Bates, Catherine W Ernst, Nancy E Raney and Juan P Steibel. 2014. Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations. BMC Bioinformatics, 15:246.

chenchunyu88/BATools documentation built on May 19, 2019, 8:21 a.m.