Compute the pairwise similarity matrix of the given term list.

kobas.term_similarity {KOBAS}

R Documentation

Compute the pairwise similarity matrix of the given term list.

Description

Usage

kobas.term_similarity(terms,
    method = "kappa",
    universe = -1);

Arguments

terms

a named list of the character vectors, the name of each slot is the term id and the value is the member gene id vector of that term (for example the result of as.geneSet of a gsea background model). [as list]

method

the similarity method: kappa (Cohen's kappa, default) or jaccard. [as string]

universe

the size of the gene universe that is used by the kappa method. Default -1 means the union size of all of the given terms. [as integer]

env

the R# runtime environment. [as Environment]

Authors

gseakit

Value

a dataframe of the similarity matrix, both the row names and the column names are the term ids and the diagonal values are 1.

clr value class

dataframe

[Package KOBAS version 1.0.0.0 Index]