get_homology_matrix_new: get_homology_matrix_new

In humayun2017/SPAGI2: SPAGI2: Identification of active signalling pathways for cross-species by integrating gene expression and human protein interaction network

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_new(
  species1,
  species2,
  homology.table,
  seq.identity = FALSE
)

Arguments

species1	Species 1 name, in the form 'hsapiens'
species2	Species 2 name, in the form 'hsapiens'
homology.table	Homology table for two species
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.homology.table<-get_homology_table_new('hsapiens','drerio')
human.zebrafish.homology.matix <- get_homology_matrix_new('hsapiens','drerio', human.zebrafish.homology.table)
print(data.matrix(human.zebrafish.homology.matix[1:5,1:5]))

humayun2017/SPAGI2 documentation built on Aug. 5, 2020, 12:06 a.m.