sponge_gene_miRNA_interaction_filter: ERROR::e: $ operator is invalid for atomic vectors

Hi,

I'm running the code with my dataset, and the first function "sponge_gene_miRNA_interaction_filter" returns the following error:

[image](https://github.com/biomedbigdata/SPONGE/assets/58339510/a1126638-33fc-4a0e-afbe-2b98d0642dc0)

my data is organized in the form:
normalized_counts_mRNA: matrix with patients in rows (n = 28) x genes in columns (n = 1013)
normalized_counts_miRNA: matrix with patients in rows (n = 28) x miRNAs in columns (n = 140)
adj_mx: interaction matrix with genes in rows (n = 1013) x miRNAs in columns (n = 140)

I was looking in the github for a better description of the function, to see where it could be happening this error, but i do not found and do not know what to do, I would be very grateful if you guys could help me with this issue.

Start at the sponge_gene_miRNA_interaction_filter entry point and reproduce the error with the three matrix inputs and dimensions described in the issue. Trace the failing `$` access and determine the function’s expected input objects; done means the reported dataset structure is handled without this error and the expected inputs are clear.

Written by the indexing model from the issue text.