make_smpdb_glist: Make a feature list for SMPDB pathways.

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

Make a feature list for SMPDB pathways.

Description

Make a feature list for SMPDB pathways.

Usage

make_smpdb_glist(
  smpdb.tab,
  annot,
  id.cols.smpdb = c("Metabolite.ID", "ChEBI.ID", "KEGG.ID"),
  id.cols.annot = c("HMDB", "ChEBI", "KEGG"),
  pwys.name.col = "Pathway.Name",
  pwys.id.col = "SMPDB.ID",
  pwys.type.col = "Pathway.Type",
  pwys.type = "Metabolic"
)

Arguments

smpdb.tab	A dataframe of SMPDB data, whith column names in id.cols.smpdb, pwys.name.col, and pwys.id.col.
annot	Metabolite annotation, with column names in id.cols.annot
id.cols.smpdb	Column names in smpdb.tab for HMDB, ChEBI, and KEGG IDs.
id.cols.annot	Column names in annot for HMDB, ChEBI, and KEGG IDs.
pwys.name.col	Column name in smpdb.tab for pathway names.
pwys.id.col	Column name in smpdb.tab for pathway IDs.
pwys.type.col	Column name in smpdb.tab for pathway types.
pwys.type	Type of pathways to use. Default is "Metabolic".

Value

A list

jdreyf/jdcbioinfo documentation built on April 15, 2024, 6:37 p.m.