get_functional_similarity: get_functional_similarity()

In priesgo/TCGAome: MultiOmics (just RNAseq and RPPA...) Data Analyzer on TCGA data

Description

Function that gets the functional similarity between two terms. That is a measure of the shared terms in the annotations resources. This functional similarity is implemented as a distance between binary vectors.

Usage

get_functional_similarity(x, term1, term2, distance_measure)

Arguments

x	The GeneAnnotations class on which the method will run.
term1	The first term on which to calculate the functional similarity.
term2	The second term on which to calculate the functional similarity.
distance_measure	The binary distance method (one of UI, binary, bray-curtis, cosine)

Value

The functional similarity between term1 and term2

Examples

kegg <- TCGAome::load_kegg()
random_kegg_term1 = kegg@term2gene$Term[runif(1, max = length(kegg@term2gene$Term))]
random_kegg_term2 = kegg@term2gene$Term[runif(1, max = length(kegg@term2gene$Term))]
get_functional_similarity(kegg, random_kegg_term1, random_kegg_term2, "cosine")
get_functional_similarity(kegg, random_kegg_term1, random_kegg_term2, "binary")
get_functional_similarity(kegg, random_kegg_term1, random_kegg_term2, "UI")
get_functional_similarity(kegg, random_kegg_term1, random_kegg_term2, "bray-curtis")

priesgo/TCGAome documentation built on May 25, 2019, 11:26 a.m.