path_enrichmentscore: Calculates pathway enrichment score of the pathways linked to...

In metabolomicsworkbench/MetENP: Metabolite enrichment analysis and their associated enriched pathways

Calculates pathway enrichment score of the pathways linked to significant metabolites

Description

Calculates pathway enrichment score of the pathways linked to significant metabolites

Usage

path_enrichmentscore(
  met_path,
  sig_metabolite_kegg_id,
  ls_path,
  refmet_class,
  sps,
  padj,
  kegg_comp_path = FALSE
)

Arguments

met_path	dataframe of pathways mapped to significant metabolites as obtained from met_pathways
sig_metabolite_kegg_id	dataframe of significantly altered metabolites for HG calculation
ls_path	list of all the KEGG compounds linked to pathways. This can be obtained by running comp_linkedto_pathways().R or is also available please use ls_path when you want to calculate HG score depending on all the compounds in KEGG linked to a pathway sysdata.rda
refmet_class	dataframe of metabolite data with refmet class for a study, alternatively, data obtained from rest can also be given here which is yet not associated to refmet class We need this to get the number of all the metabolites detected in the study for calculating HG score.
sps	species name
padj	Method for p value adjustment, i.e. "fdr"
kegg_comp_path	TRUE or FALSE depending you want to use the ls_path as your background. Default is FALSE, where background set is the total metabolite in a study

Examples

kegg_es = path_enrichmentscore(met_path,sig_metabolite_kegg_id, ls_path,refmet_class,sps='hsa',padj='fdr')

metabolomicsworkbench/MetENP documentation built on April 12, 2025, 7:55 p.m.