metaponeResult-class: Class "metaponeResult"

In tianwei-yu/metapone: Conducts pathway test of metabolomics data using a weighted permutation test

Class "metaponeResult"

Description

This class represents the results of pathway testing. The testing result contain two major components: the significant level of each pathway, and the features matched to each pathway.

Objects from the Class

Objects can be created by calls of the form new("metaponeResult", ...).

Slots

test.result:

a dataframe containing p_value, n_significant metabolites, n_mapped_metabolites, n_metabolites, significant metabolites, mapped_metabolite IDs, lfdr and pathway name.

mapped.features:

A list containing n entries, where n is the number of pathways. Each entry is a data frame, containing the features mapped to this pathway. The information include m.z, retention.time, p.value, statistic, HMDB_ID, theoretical m.z, ion.type, fractional counts.

Methods

ptable

signature(object = "metaponeResult"): return the data.frame of test statistics for each pathway, including p_value, n_significant metabolites, n_mapped_metabolites, n_metabolites, significant metabolites, mapped_metabolite IDs lfdr and and pathway name.

ftable

signature(object = "metaponeResult"): Returns a list containing the mapped features in each pathway. Each pathway is represented by a data.frame as an item in the list object. The dataframe include information of m.z, retention.time, p.value, statistic, HMDB_ID, theoretical m.z, ion.type, fractional counts.

Author(s)

Tianwei Yu

tianwei-yu/metapone documentation built on Aug. 21, 2022, 3:09 a.m.