metapone {metapone}R Documentation

METAbolic pathway testing using both POsitive and NEgative mode data

Description

Metapone conducts pathway tests for untargeted metabolomics data. It has three main characteristics: (1) expanded database combining SMPDB and Mummichog databases, with manual cleaning to remove redundancies; (2) A new weighted testing scheme to address the issue of metabolite-feature matching uncertainties; (3) Can consider positive mode and negative mode data in a single analysis.

Usage

metapone(pos = NULL, neg = NULL, pa, hmdbCompMZ, pos.adductlist = 
c("M+H", "M+NH4", "M+Na", "M+ACN+H", "M+ACN+Na", "M+2ACN+H", "2M+H", 
"2M+Na", "2M+ACN+H"), neg.adductlist = c("M-H", "M-2H", "M-2H+Na", 
"M-2H+K", "M-2H+NH4", "M-H2O-H", "M-H+Cl", "M+Cl", "M+2Cl"), 
use.fractional.count = TRUE, match.tol.ppm = 5, p.threshold = 0.05, 
n.permu = 200, fractional.count.power = 0.5, max.match.count = 10)

Arguments

pos

The positive ion mode test results. A matrix with four columns: m/z, retention time, p-value, test statistic. The package doesn't require both pos and neg to be present. One ion mode result is sufficient.

neg

The negative ion mode test results. A matrix with four columns: m/z, retention time, p-value, test statistic. The package doesn't require both pos and neg to be present. One ion mode result is sufficient.

pa

Pathway information. A data frame with five columns: database pathway ID, pathway name, HMDB ID, KEGG ID, category of pathway.

hmdbCompMZ

the m/z values of common adduct ions of HMDB metaboites. See the help file of hmdbCompMZ for details.

pos.adductlist

The vector of positive adduct ions to be considered.

neg.adductlist

The vector of negative adduct ions to be considered.

use.fractional.count

A lot of features match to multiple metabolites by m/z. Whether to discount such matches by using fractional counts.

match.tol.ppm

The ppm level when conducting m/z match.

p.threshold

The threshold of p-values of metabolic features to be considered significant.

n.permu

The number of permutations in permutation test.

fractional.count.power

The fractional counts are taken to this power to transform the weights.

max.match.count

When calculating fractional counts, some features might be matched to too many. In that case the number of matches is capped by the value of max.match.count.

Value

The method returns a generic S4 object of class "metapone.result":

@test.results

A matrix with 6 columns: "p_value", "n_significant metabolites", "n_mapped_metabolites", "n_metabolites", "significant metabolites", "mapped_metabolites". Each row is for a pathway.

@mapped.features

A list. Each item is for a pathway. The item lists matched significant metabolites.

Author(s)

Tianwei Yu<yutianwei@cuhk.edu.cn>)

References

https://smpdb.ca/ https://shuzhao-li.github.io/mummichog.org/software.html

See Also

hmdbCompMZ, pa

Examples

data(hmdbCompMZ.metapone)
data(pa)
data(pos)
data(neg)
r<-metapone(pos, neg, pa, hmdbCompMZ=hmdbCompMZ.metapone, p.threshold=0.05,
   n.permu=100,fractional.count.power=0.5, max.match.count=10)
hist(ptable(r)[,1])

[Package metapone version 1.0.0 Index]