get_homology_table_new: get_homology_table_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 uses information from Ensembl to generate a homology table between two species.

Usage

get_homology_table_new(species1, species2, sequence_identity_reference = 0)

Arguments

species1	Species 1 name, in the form 'hsapiens'
species2	Species 2 name, in the form 'hsapiens'
sequence_identity_reference	Flag of which sequence identity value to retrieve. 0 (default) returns no value); 1 returns the sequence of identity of genes in species 2 compared to species 1; 2 returns the sequence of identity of genes in species 1 compared to species 2.

Details

This function uses information from Ensembl to generate a homology table between two species.

Value

This function return a data frame with 2 or 3 columns, representing the Ensembl gene IDs in species 1 and 2, and the sequence identity score if requested.

Examples

human_zebrafish_homology_table <- get_homology_table_new('hsapiens', 'drerio')
head(human_zebrafish_homology_table)

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