In tidymass/metpath: Pathway analysis for metabolomics data

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

Load packages

library(metpath)
library(tidyverse)

Load KEGG pathway human database

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

get_pathway_class(kegg_hsa_pathway)

Pathway enrichment

We use the demo compound list from metpath.

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

Remove the disease pathways:

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

head(pathway_class)

remain_idx =
  pathway_class %>%
  unlist() %>%
  stringr::str_detect("Disease") %>%
  `!`() %>%
  which()

remain_idx

pathway_database =
  kegg_hsa_pathway[remain_idx]

pathway_database

result = 
enrich_kegg(query_id = query_id_kegg, 
            query_type = "compound", 
            id_type = "KEGG",
            pathway_database = pathway_database, 
            p_cutoff = 0.05, 
            p_adjust_method = "BH", 
            threads = 3)

Check the result:

result

Plot to show pathway enrichment

enrich_bar_plot(object = result)

enrich_scatter_plot(object = result)

enrich_network(object = result)

Session information

sessionInfo()

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