get_homology_matrix: get_homology_matrix

In VCCRI/XGSA: XGSA: A statistical method for cross-species gene set analysis

Description

This function creates a homology matrix between two species by retrieving the homology table and then converting it into a sparse matrix.

Usage

get_homology_matrix(species1, species2, seq.identity = FALSE)

Arguments

species1	Species 1 name, in the form 'hsapiens'
species2	Species 2 name, in the form 'hsapiens'
seq.identity	Boolean of whether or not to retrieve sequence identity information, defaults to FALSE

Details

This function creates a homology matrix between two species by retrieving the homology table and then converting it into a sparse matrix.

Value

This function returns a sparse matrix where rows represent the genes in species 1 and columns the genes in species 2.

Examples

human_zebrafish_matix <- get_homology_matrix('hsapiens','drerio')
print(data.matrix(human_zebrafish_matix[1:5,1:5]))

VCCRI/XGSA documentation built on March 5, 2021, 10:22 p.m.