In rmsharp/nprcmanager: Genetic Tools for Colony Management

Genetic Value Analysis

The Genetic Value Analysis tab provides all of the options needed for producing a genetic value analysis report. The specifics of generating the genetic value analysis report are described on the Genetic Value Analysis and Breeding Group Description tab.

When the analysis is begun, it will generate a genetic value analysis for the currently-specified population in the pedigree. If no population has been specified, the entire pedigree will go into the analysis. This can be problematic, as the function for calculating the pairwise kinship matrix cannot handle large pedigrees. The kinship calculation is known to handle pedigree files containing up to 6000 individuals. It will not, however, handle the whole ONPRC rhesus studbook (~24,000 animals). The exact maximum pedigree size is not currently known and will need to be tested. Due to these problems, the input studbook will automatically be trimmed to the ancestors of the currently-specified population before the genetic value analysis is begun.

The genome uniqueness threshold input box allows the user to specify what constitutes a 'unique' allele in the gene-drop simulation. The algorithm description later in this document provides a more in-depth explanation of how the genome uniqueness calculation uses this information. By default, the gene-drop simulation underlying the genome uniqueness calculation considers an individual as unique if no other members of the current population have inherited the same allele during an iteration of the gene-drop. This can be adjusted using the drop-down box to allow up to four other animals to have inherited the allele and still consider it unique.

After the report has been generated, it can be subset to view a specific group of the animals using the text input box. Both the currently-viewed subset and the full report can be exported to a file from here.

rmsharp/nprcmanager documentation built on April 24, 2021, 3:13 p.m.