Python Genomic Selection functions

Miguel Perez-Enciso ([email protected])

Installation

Download or clone the repository.

Quick startup

Check the jupyter notebook (main.ipynb) and main.py script

Input files

Inputs are:

• a nsnp x nind genotype file coded as 0, 1, 2 for each genotype.

• a pedigree and phenotypes file, with inds coded as integers 1,2.. nind, 0 for unknwon parents, followed by phenotype values:

       id   id_father   id_mother   y1   y2 ...
  

Coding for missing values

• No missing values are allowed in genotypes matrix.

• For phenotypes, the missing code is -999999. An alternative is to set the vector yIds. This vector is an integer vector with indices of individuals containing individuals without missing phenotypes. For instance, in calling the main function

        gs.doEbv0(criterion, X, y, yIds, h2, ped)
  

criterion is the evaluation ciriterion ('blup', 'gblup', 'sstep'), X is the matrix with genotypes, y is a nind x ntrait matrix with ntrait phenotypes, yIds contains id indices (eg yIds = [0, 3, 9]) means that inds 1st, 4th and 10th have phenotypes, and ped is the pedigree.

Citation

Please cite this if you use or reuse the code:

M. Perez-Enciso, L.C. Ramirez-Ayala, L.M. Zingaretti. SeqBreed: a python tool to evaluate genomic prediction in complex scenarios. To be submitted.

How to contribute

Please send comments, suggestions or report bugs to [email protected]. From 2020 on, I will be working at INIA in Madrid (Spain), check at www.inia.es or in the internet for my new email.