mseapca (version 2.0.3)

pathbank2list: 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)

Value

list of metabolite or protein set

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

Author

Hiroyuki Yamamoto

Details

AHPathbankDbs needs to be installed separately.

Examples

if (FALSE) {
## 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)
}