cpdidmap: Mapping between compound IDs and KEGG accessions

In pathview: a tool set for pathway based data integration and visualization

Description

These auxillary compound ID mappers connect KEGG compound/glycan/drug accessions to compound names/synonyms and other commonly used compound-related IDs.

Usage

cpdidmap(in.ids, in.type, out.type)
cpd2kegg(in.ids, in.type)
cpdkegg2name(in.ids, in.type = c("KEGG", "KEGG COMPOUND accession")[1])
cpdname2kegg(in.ids)

Arguments

in.ids	character, input IDs to be mapped.
in.type	character, the input ID type, needs to be either "KEGG" (including compound, glycan and durg) or one of the compound-related ID types used in CHEMBL database. For a full list of the CHEMBL IDs, do data(rn.list); names(rn.list). For cpdkegg2name), default in.type = "KEGG".
out.type	character, the output ID type, needs to be either "KEGG" (including compound/glycan/durg) or one of the compound-related ID types used in CHEMBL database. For a full list of the CHEMBL IDs, do data(rn.list); names(rn.list).

Details

character, the output ID type, needs to be either "KEGG" or one of the compound-related ID types used in CHEMBL database. For a full list of the CHEMBL IDs, do data(rn.list); names(rn.list).

KEGG has its own compound ID system, including compound (glycan/durg) accessions. Therefore, all compound data need to be mapped to KEGG accessions when working with KEGG pathways. Function cpd2kegg does this mapping by calling cpdname2kegg or cpdidmap. On the other hand, we frequently want to check or show compound full names or other commonly used IDs instead of the less informative KEGG accessions when working with KEGG compound nodes, Functions cpdkegg2name and cpdidmap do this reverse mapping. These functions are written as part of the Pathview mapper module, they are equally useful for other compound ID or data mapping tasks. The use of these functions depends on a few data objects: "cpd.accs", "cpd.names", "keg.met" and "rn.list", which are included in this package. To access them, use data() function.

Value

a 2-column character matrix recording the mapping between input IDs to the target ID type.

Author(s)

Weijun Luo <[e-mail]>

References

Luo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integration and visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285

See Also

eg2id and id2eg the auxillary gene ID mappers, mol.sum the auxillary molecular data mapper, node.map the node data mapper function.

Examples

data(cpd.simtypes)
#generate simulated compound data named with non-KEGG ("CAS Registry Number")IDs
cpd.cas <- sim.mol.data(mol.type = "cpd", id.type = cpd.simtypes[2], 
    nmol = 10000)
#construct map between non-KEGG ID and KEGG ID ("KEGG COMPOUND accession")
id.map.cas <- cpdidmap(in.ids = names(cpd.cas), in.type = cpd.simtypes[2], 
    out.type = "KEGG COMPOUND accession")
#Map molecular data onto standard KEGG IDs
cpd.kc <- mol.sum(mol.data = cpd.cas, id.map = id.map.cas)
#check the results
head(cpd.cas)
head(id.map.cas)
head(cpd.kc)

#map KEGG ID to compound name
cpd.names=cpdkegg2name(in.ids=id.map.cas[,2])
head(cpd.names)

pathview documentation built on May 2, 2019, 4:56 p.m.