Determining the effect of dataset size in results

Question

[a_confused_biologist]

I have two datasets of metabolic reactions, let's say A and B. A is part of B and, therefore, A is smaller than B.

The data contain three columns (metabolite, enzyme, reaction type).

I would like to run the same analysis with both datasets and compare any potential differences in the results. How could I test whether it is the size of B that plays a role in these differences or the additional information it carries?

I believe a permutation test with resuffling of labels (metabolites and enzymes) would help me clarify that. but how do I set this up in R?

Thank you in advance!!