metapone {metapone} | R Documentation |
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.
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)
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. |
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. |
Tianwei Yu<yutianwei@cuhk.edu.cn>)
https://smpdb.ca/ https://shuzhao-li.github.io/mummichog.org/software.html
hmdbCompMZ, pa
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])