Description Usage Arguments Value References See Also Examples
This function calculates genome content similarity index for two genomes gene set by gene set.
1 | similarity_by_set(gene_sets1, gene_sets2)
|
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. |
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.
Kamneva OK. Genome composition of microbes predicts their co-occurrence in the environment. In review.
similarity
, functional_association
, set_representation
,
reference_gene_sets
.
1 2 3 4 5 6 | 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)
|
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