metPathway: metPathway

metPathwayR Documentation

metPathway

Description

Metabolic pathway analysis.

Usage

metPathway(annotation.result = "ms2.match.annotation.result.csv", group,
  max.isotope = 4, uni.test = c("t", "wilcox", "anova"),
  column = c("hilic", "rp"), polarity = c("positive", "negative"),
  path = paste(file.path(".", "MRN_annotation_result"), ifelse(polarity ==
  "positive", "POS", "NEG"), sep = "_"), output.path = paste(file.path(".",
  "Dysregulated_network_analysis_result"), ifelse(polarity == "positive", "POS",
  "NEG"), sep = "_"), correct = TRUE, p.cutoff = 0.01, mz.tol = 25,
  rt.tol1 = 3, rt.tol2 = 30, cor.tol = 0, int.tol = 500, threads = 3,
  species = c("hsa", "dme", "mmu", "rat", "bta", "gga", "dre", "cel", "sce",
  "ath", "smm", "pfa", "tbr", "eco", "ppu", "syf"), use.all.kegg.id = FALSE,
  only.mrn.annotation = FALSE, use.old.null = FALSE)

Arguments

annotation.result

Annotation.result from ms2Annotation.

group

The group you want to use.

max.isotope

The max number of isotope.

uni.test

The method of univariate test.

column

hilic or rp.

polarity

positive or negative.

path

The work directory.

output.path

The directory for outputting results.

correct

Correct p value or not.

p.cutoff

The cutoff of p value. Default is 0.01.

mz.tol

The mz tolerance of KEGG matching. Defalut is 25 ppm.

rt.tol1

The RT tolerance of isotope annotation (second). Default is 3 s.

rt.tol2

The RT tolerance of KEGG matching (%). Default is 30%.

cor.tol

THe tolerance of correlation.

int.tol

The tolerance of intensity ratio for isotope annotation(%).

threads

The number of threads.

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.

use.all.kegg.id

Use all annotations from KEGG database. Default is FALSE.

only.mrn.annotation

Only use MEN annotations or not.

use.old.null

Use old null distribution of not. Default is FALSE.

Author(s)

Xiaotao Shen shenxt@sioc.ac.cn


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