pathbank2list {mseapca} | R Documentation |
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
## 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)
[Package mseapca version 2.2.1 Index]