metPathway2: metPathway2

In ZhuMSLab/MetDNA: MetDNA

metPathway2

Description

Metabolic pathway analysis.

Usage

metPathway2(annotation.result.pos = "ms2.match.annotation.result.csv",
  annotation.result.neg = "ms2.match.annotation.result.csv", group,
  max.isotope = 4, uni.test = c("t", "wilcox", "anova"),
  column = c("hilic", "rp"), pos.path = file.path(".", "POS"),
  neg.path = file.path(".", "NEG"), output.path = file.path(".",
  "POS and NEG", "Dysregulated_network_analysis_result"), correct = TRUE,
  p.cutoff = 0.01, mz.tol = 25, rt.tol1 = 3, rt.tol2 = 30,
  cor.tol = 0, int.tol = 500, threads = 3, use.old.null = FALSE,
  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)

Arguments

annotation.result.pos	Positive annotation.result from ms2Annotation.
annotation.result.neg	Negative 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.
pos.path	The positive directory.
neg.path	The negative directory.
output.path	The directory to output results.
correct	Correct p value or not.
p.cutoff	The cutoff of p value.
mz.tol	The mz tolerance of KEGG matching.
rt.tol1	The RT tolerance of isotope annotation (second).
rt.tol2	The RT tolerance of KEGG matching (%).
cor.tol	THe tolerance of correlation.
int.tol	The tolerance of intensity ratio (%).
threads	The number of threads.
use.old.null	Use old null distribution of not.
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.

Author(s)

Xiaotao Shen [e-mail]

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