metPathway: metPathway

In ZhuMSLab/MetDNA: MetDNA

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 [e-mail]

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