FindPathway: Find, for every compound, his pathways using multiple...

In cherkaos/MetabToPathways: Query metabolites to find their pathways, for multiple databases (Kegg, SMPDB, HMDB and Biocyc)

Description

Function to find, for every compound, his pathways using the 4 databases, using soecific id. Returns different id and pathway of every compound to get the best coverage.

Usage

FindPathway(name, puchem, kegg)

Arguments

name	List of name of every compounds to query.Should be the same length as puchem and kegg. Accept names that are blank.
puchem	List of puchem id of every compounds to query.Should be the same length as name and kegg. Accept puchem id that are blank.
kegg	List of kegg id of the compounds to query.Should be the same length as puchem and name. Accept kegg id that are blank.

Details

The same position in the 3 lists should repesent the same compound but with different id. A compound can be find with his puchem, name or kegg. Can accept id's that are blanks.

Value

Returns a list of information for every compound.

Name	Name of compound as character
Pubchem	Pubchem id of compound as character
HMDB	HMDB id of compound as character
KeggID	Kegg id of compound as character
BioCyc	Biocy id of compound as character
InchiKey	Inchikey of compound as character
Map	Map of the 1st pathway of the list
KeggPathway	List of pathway from Kegg where the compound is found
KeggPathID	Kegg id of the 1st pathway of the list
SmpdbPathway	List of pathway from SMPDB where the compound is found
HmdbPathway	List of pathway from HMDB where the compound is found
BiocycPathway	List of pathway from Biocyc where the compound is found

Author(s)

Sarah Cherkaoui

References

Kegg: Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000 Jan 1;28(1):27-30.

SMPDB: Wishart DS, Frolkis A, Knox C, et al., SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 2010 Jan;38(Database issue):D480-7

HMDB: Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6

Biocyc: Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A,Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010 Jan;38(Database issue):D473-9.

Examples

## The function is currently defined as
FindPathway (list$name, list$puchem, list$kegg) 

cherkaos/MetabToPathways documentation built on May 13, 2019, 3:54 p.m.