similarity_by_set: Compute genome content similarity by gene set

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

Description

This function calculates genome content similarity index for two genomes gene set by gene set.

Usage

similarity_by_set(gene_sets1, gene_sets2)

Arguments

gene_sets1	list of vectors of 1s and 0s which represnet presence and absence of gene families from each of the gene sets in first genome.
gene_sets2	list of vectors of 1s and 0s which represnet presence and absence of gene families from each of the gene sets in second genome.

Value

A data frame with 5 variables: set_ID gene set identifier, score genome content similarities computed between gene_sets1 and gene_sets2 for each individual gene set, set_size number of gene families in the gene set, in_genome1 number of gene families from gene set present in first and in_genome2 second genomes.

References

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

See Also

similarity, functional_association, set_representation, reference_gene_sets.

Examples

data(families_Bf)
data(families_Er)
sets_Bf = set_representation(families = families_Bf, gene_sets = reference_gene_sets)
sets_Er = set_representation(families = families_Er, gene_sets = reference_gene_sets)
sim_Bf_Er = similarity_by_set(gene_sets1 = sets_Bf, gene_sets2 = sets_Er)
head(sim_Bf_Er)

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