metEnrichment: metEnrichment

metEnrichmentR Documentation

metEnrichment

Description

Metabolic enrichment analysis.

Usage

metEnrichment(annotation.table, sample.pos, sample.neg, group,
  column = c("hilic", "rp"), candidate.num = 5, sample.info = sample.info,
  polarity = c("positive", "negative", "both"), species = c("hsa", "dme",
  "mmu", "rat", "bta", "gga", "dre", "cel", "sce", "ath", "smm", "pfa", "tbr",
  "eco", "ppu", "syf"), pos.path = pos.path, neg.path = neg.path,
  output.path = output.path)

Arguments

annotation.table

The metabolite annotation result which used for pathway enrichment analysis. The data frame should contain two column, the column names are peak.name and KEGG.ID.

sample.pos

Positive annotation.result from ms2Annotation.

sample.neg

Negative annotation.result from ms2Annotation.

group

The group you want to use.

column

Column, "hilic" or "rp".

candidate.num

Top candidate.num metabolites for each peak.

sample.info

Sample information.

polarity

The polarity mode of data. "positive", "negative" or "both".

species

The species. "hsa" is Homo sapiens (human), "dme" is Drosophlia melanogaster (fruit fly), "mmu" is Mus musculus (mouse), "rat" is Rattus norvegicus (rat), "bta" is Bos taurus (cow), "gga" is Gallus domesticus (chicken), "dre" is Danio rerio (zebrafish), "cel" is Caenorharomyces elegans (nematode), "sce" is Saccharomyces cerevisaiae (yeast), "ath" is Arabidopsis thaliana (thale cress), "smm" is Schistosoma mansoni, "pfa" is Plasmodum falciparum 3D7, "tbr" is Trypanosoma brucei, "eco" is Escherichia coli K-12 MG1655, "ppu" is Pseudomonas putida KT2440, "syf" is Synechococcus elongatus.

pos.path

Directory of positive results.

neg.path

Directory of negative results.

output.path

The directory to output results.

Author(s)

Xiaotao Shen shenxt@sioc.ac.cn


ZhuMSLab/MetDNA documentation built on March 29, 2022, 5:45 p.m.