This method lets you extract the pangenome matrix of the pangenome. It is not possible to directly change the pangenome matrix as it not necessary stored in the object but might be calculated on request. Either way the pangenome matrix is a function of the gene grouping and should be changed by changing the gene grouping instead of being manipulated downstream.
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A pgVirtual subclass
A matrix with organisms as columns and gene groups as rows
pgVirtual: Get pangenome matrix for pgVirtual subclasses
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