Manipulate and check pedigree file and calculate the triplet format of pedigree relationship matrix (A-matrix)
The R script in this repository evaluates the pedigree data based on the following process:
- Pedigree Preparation using prePed function in optiSel package
- Checking the completeness of the pedigree for the intended evaluation and identifying individuals with sufficient pedigree information. The following parameters were computed for each individual during the pedigree investigation:
- equiGen: Number of equivalent complete generations, calculated as the sum of the proportion of known ancestors over all generations traced
- fullGen: Number of fully traced generations
- maxGen: Number of maximum generations traced
- PCI: Index of pedigree completeness, which is the harmonic mean of the pedigree completenesses of the parents (MacCluer et al, 1983)
- Inbreeding: Pedigree-based inbreeding coefficient
- Calculating pedigree-based relationship matrix (A matrix) using nadiv package and converting the sparse matrix to triplet format.