pathbank2list: Generate metabolite set list from PathBank database

In mseapca: Metabolite Set Enrichment Analysis for Loadings

Generate metabolite set list from PathBank database

Description

This function generates metabolite set list of PathBank database by referencing the AHPathbankDbs Bioconductor package.

Usage

pathbank2list(tbl_pathbank, subject, id)

Arguments

tbl_pathbank	tibble from AHPathbankDbs
subject	Pathway subject (Metabolic, Disease, etc.) in tibble
id	database ID (HMDB ID, Uniprot ID, etc.) used for analysis

Details

AHPathbankDbs needs to be installed separately.

Value

list of metabolite or protein set

Author(s)

Hiroyuki Yamamoto

Examples

## Not run: 
## PathBank
library(AnnotationHub)

ah <- AnnotationHub()
qr <- query(ah, c("pathbank", "Homo sapiens"))

#tbl_pathbank <- qr[[1]] # metabolomics
tbl_pathbank <- qr[[2]] # proteomics

ids <- names(tbl_pathbank)[-c(1:4)]
id <- ids[1] # Uniprot ID

subs <- unique(tbl_pathbank$`Pathway Subject`)
subject <- subs[6] # Protein

M <- pathbank2list(tbl_pathbank, subject, id)

## End(Not run)

mseapca documentation built on Nov. 4, 2023, 5:06 p.m.