Description Usage Arguments Value References See Also Examples
This function calculates genome content similarity index for two genomes.
1 | similarity(gene_sets1, gene_sets2, threshold = 0.05, size = 4)
|
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. |
threshold |
fraction of gene families from a gene set which is required to be present in at least one of the genomes for for the gene set to contribute to genome content similarity index calculation (default is 0.05). |
size |
minimal size of the gene set to consider (default is 4). |
Genome content similarity index computed for two genomes encoding gene_sets1
and gene_sets2
respectively.
Kamneva OK. Genome composition of microbes predicts their co-occurrence in the environment. In review.
similarity_by_set
, 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(gene_sets1 = sets_Bf, gene_sets2 = sets_Er, threshold = 0.05, size = 4)
sim_Bf_Er
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.