set_representation: Calculate gene set representation

In olgakamneva/genomics2ecology: Methods of genomic analysis for microbial ecology

Description

This function calculates presence and absence of gene families in each of the reference gene set in a genome from the list of gene family encoded in that genome.

Usage

set_representation(families, gene_sets = reference_gene_sets)

Arguments

families	character vector of gene family names from STRING 10.0 present in first genome.
gene_sets	list of character vectors. Each individual vector represents a set of functionally associated gene families (or gene set) likely involved in the same function or process.

Value

Microbe-microbe functional association index for two genomes which encode families1 and families1.

References

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

See Also

similarity, similarity_by_set.

Examples

data(families_Bf)
sets_Bf = set_representation(families = families_Bf, gene_sets = reference_gene_sets)

olgakamneva/genomics2ecology documentation built on May 24, 2019, 12:51 p.m.