functional_association: Compute microbe-microbe functional association index
In olgakamneva/genomics2ecology: Methods of genomic analysis for microbial ecology

Description Usage Arguments Value References See Also Examples

This function calculates microbe-microbe functional association index for two genomes.

1	functional_association(families1, families2, network = reference_network)

`families1`	character vector of gene family names from STRING 10.0 present in first genome.
`families2`	character vector of gene family names from STRING 10.0 present in second genome.
`network`	data frame encoding associations between gene families. Should contain 2 or 3 variables: `node1` gene family one, `node2` gene family two, `weight` weight of the edge.

Microbe-microbe functional association index for two genomes which encode families1 and families1. This index represents fraction of edges which connect gene families present in one of the compared genomes to gene families present in another out of all of the edges in the gene family network encoded by one of the two genomes exclusively.

Kamneva OK. Genome composition of microbes predicts their co-occurrence in the environment. In review.

similarity, similarity_by_set.

data(families_Bf)
data(families_Er)
association_index = functional_association(families1 = families_Bf, families2 = families_Er, network = reference_network)
association_index