In tidymass/metpath: Pathway analysis for metabolomics data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)

library(metpath)
library(tidyverse)

Load HMDB pathway database

data("hmdb_pathway", package = "metpath")
hmdb_pathway

get_pathway_class(hmdb_pathway)

Pathway enrichment

We use the demo compound list from metpath.

data("query_id_hmdb", package = "metpath")
query_id_hmdb

Only remain the Metabolic;primary_pathway.

#get the class of pathways
pathway_class = 
  metpath::pathway_class(hmdb_pathway) 

remain_idx = which(unlist(pathway_class) == "Metabolic;primary_pathway")

remain_idx

hmdb_pathway = 
  hmdb_pathway[remain_idx]

hmdb_pathway

result = 
enrich_hmdb(query_id = query_id_hmdb, 
            query_type = "compound", 
            id_type = "HMDB",
            pathway_database = hmdb_pathway,
            only_primary_pathway = TRUE,
            p_cutoff = 0.05, 
            p_adjust_method = "BH", 
            threads = 3)

Check the result:

result

Plot to show pathway enrichment

enrich_bar_plot(
  object = result,
  x_axis = "p_value_adjust",
  cutoff = 0.05,
  top = 10
)

enrich_scatter_plot(object = result)

enrich_network(object = result)

tidymass/metpath documentation built on July 21, 2023, 3:11 p.m.