kangar00: set_names-matrix-method – R documentation

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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)

Usage

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

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

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`.
`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`.

Value

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

Author(s)

Stefanie Friedrichs

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

v1.4

GPL-2

Authors

Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut], Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb], Heike Bickeboeller [ctb]

Initial release

2020-02-12