- Pedigree Sort Module (PSM): sorts the pedigree file, containing parentage information, by correcting duplicated or missing entries so that no progeny appears after its parents.
- Pedigree-based Relationship Matrix Calculation Module (PRM): generates the pedigree-based additive and dominance relationship matrices based on the expected proportions of identical-by-descent (IBD) loci across genome of any pair of individuals.
- Quality Control Module (QCM): refines the input genotyping data based on multiple user-specified quality control measures.
- Genomic Relationship Matrix Calculation Module (GRM): generates the genomic additive and dominance relationship matrices based on the observed IBD proportions across the genotyped loci of any pair of individuals.
- Epistatic Matrix Calculation Module (EMM): generates the pedigree-based and genomic epistatic relationship matrices.
- Inverse Matrix Calculation Module (IMM): generates the inverse of relationship matrices and deals with matrix singularity issue.
- Pedigree Manipulation Module (PMM): aligns, merges and compares the pedigree-based and genomic relationship matrices, or adjusts the genomic relationship matrices.
- Genetic Prediction Module (GPM): predicts unobserved responses given availability of the response values for a portion of subjects under consideration and a relationship matrix for the entire set of subjects (i.e. with and without response values).
GenoMatrix is distributed as a Windows 64bit executable. It is available for data analysis to research community and commercial users free of charge. However, users are required to properly cite the copyright holders. The downloadable package contains the compiled application, the user guide and a set of simulated datasets for testing the package functionality.
The following additional data files are available for download:
- DATA.zip: Sample data
- Files S1-S4: Relationship matrices generated by different packages using sample datasets
Users need to download the compatible MATLAB Runtime [i.e. MCR version 9 (R2015b) for Windows 64-bit] from the MathWorks website and follow the installation wizard to install it if:
- MATLAB is not installed on their machines, or
- The version of installed MATLAB MCR on their machines is anything except 9 (R2015b)