cpdidmap {pathview} | R Documentation

## Mapping between compound IDs and KEGG accessions

### 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 <luo_weijun@yahoo.com>

### 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)

[Package pathview version 1.34.0 Index]