kangar00 (version 1.4.2)

set_names,matrix-method: Helper function to translate gene numbers to names

Description

This function exchanges the numbers used for genes in KEGG download KGML files with the corresponding gene names. Names are set to be the column names and rownames of the pathway's network matrix. The function is called by get_network_matrix. (For internal use)

This function exchanges the numbers used for genes in KEGG download KGML files with the corresponding gene names. Names are set to be the column names and rownames of the pathway's network matrix. The function is called by get_network_matrix. (For internal use)

Usage

# S4 method for matrix
set_names(x, nodes, my_list)
# S4 method for matrix
set_names(x, nodes, my_list)

Value

A matrix representing the interaction network in the pathway with gene names as rownames and columnnames.

A matrix representing the interaction network in the pathway with gene names as rownames and columnnames.

Arguments

x

A matrix representing the network matrix.

nodes

A vector of gene numbers to be replaced by names.

my_list

A data.frame listing gene names and numbers. Output from gene_name_number.

Author

Stefanie Friedrichs