Hello all thanks for your help! I am reposting a previous problem to simplify through analogy. I have a very complicated biologic data set. I am having memory issues, what is the best way to solve the problem below:

Attempt at a non biology analogy: ... you're in a warehouse with X closets.

Each closet has H tie hangers (H can be different for each closet) .

Each tie hanger has M rungs or hooks (M can be different as well). Then by some process ties are placed on some of the hooks (there are only as many hooks as ties placed the only important number is how many ties per hanger).

I need to read in a file with the data of ties/mutations per hanger/amino_acid_position per closet/gene, and then fill an AoA which is rows X and columns H1-Hn_sub_x. In each cell I need M ties/mutations (([x][N_sub_x]=M) ) . This structure will allow me perform the right statistical test.

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