ptable: Acessor functions for the test result table in a...
In tianwei-yu/metapone: Conducts pathway test of metabolomics data using a weighted permutation test

ptable

R Documentation

Acessor functions for the test result table in a metaponeResult object.

Description

return the data.frame of test statistics for each pathway.

Usage

## S4 method for signature 'metaponeResult'
ptable(object)

Arguments

object

A metaponeResult object.

Details

Includes p_value, n_significant metabolites, n_mapped_metabolites, n_metabolites, significant metabolites, mapped_metabolite IDs and pathway name.

Value

The method returns a data frame with 6 columns: "p_value", "n_significant metabolites", "n_mapped_metabolites", "n_metabolites", "significant metabolites", "mapped_metabolites".

Author(s)

Tianwei Yu <yutianwei@cuhk.edu.cn>

Examples

data(hmdbCompMZ.metapone)
data(pa)
data(pos)
data(neg)
dat <- list(pos, neg)
type <- list("pos", "neg")
r<-metapone(dat, type, pa, hmdbCompMZ=hmdbCompMZ.metapone, 
   p.threshold=0.05,n.permu=100,fractional.count.power=0.5, max.match.count=10)
head(ptable(r))

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