extract-pathway_database: [ method

In tidymass/metpath: Pathway analysis for metabolomics data

[ method

Description

Returns pathway IDs from a 'pathway_database' object.

Returns the number of pathways in a 'pathway_database' object.

Extracts database metadata from a 'pathway_database' object.

Extracts pathway IDs from a 'pathway_database' object.

Extracts pathway names from a 'pathway_database' object.

Extracts pathway descriptions from a 'pathway_database' object.

Extracts pathway classification from a 'pathway_database' object.

Extracts lists of genes involved in pathways from a 'pathway_database' object.

Extracts lists of compounds involved in pathways from a 'pathway_database' object.

Extracts literature references for pathways in a 'pathway_database' object.

Extracts disease associations from a 'pathway_database' object.

Extracts related modules from a 'pathway_database' object.

Usage

## S3 method for class 'pathway_database'
x[i, ...]

## S3 method for class 'pathway_database'
names(x)

## S3 method for class 'pathway_database'
length(x)

database_info(object, ...)

pathway_id(object, ...)

pathway_name(object, ...)

describtion(object, ...)

pathway_class(object, ...)

gene_list(object, ...)

compound_list(object, ...)

reference_list(object, ...)

related_disease(object, ...)

related_module(object, ...)

Arguments

x	A 'pathway_database' class object.
i	i
...	other parameters
object	A 'pathway_database' class object.

Value

pathway_database

A vector of pathway IDs.

An integer indicating the number of pathways.

A list containing database metadata.

A character vector of pathway IDs.

A character vector of pathway names.

A character vector of pathway descriptions.

A character vector of pathway classes.

A list of gene sets for each pathway.

A list of compound sets for each pathway.

A list of references for each pathway.

A list of related diseases for each pathway.

A list of related modules for each pathway.

Author(s)

Xiaotao Shen [e-mail]

Xiaotao Shen ([e-mail])

tidymass/metpath documentation built on June 1, 2025, 10:05 p.m.