Comments (1)
qmarcou
commented on July 25, 2024
Hi Wout,
This combination of three edges in the graph allows to learn the joint probability P(V,D,J). Because IGoR treats all alleles as different genes, this joint probability is useful to capture the fact that some alleles of the same gene might not be able to recombine together as they lie on different chromosomes. In a nutshell this is needed to fine tune a model to an individual of interest.
The version used by OLGA learns the factorized version P(V)P(D,J) of the gene usage probability. It will miss all information from the chromose organisation/partition of the alleles. Learning at least the P(D,J) joint probability is essential to learn the biological impossibility to recombine J2 with D2. As I am not responsible for OLGA support/developpment I cannot tell why they made the choiceof having only this conditionnal dependence, and this migth be due to some algorithmic issue...
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