cpd.accs {pathview} | R Documentation

## Mapping data between compound or gene IDs and KEGG accessions

### Description

Mapping data between compound or gene IDs and KEGG accessions

### Usage

    data(cpd.accs)
    data(cpd.names)
    data(kegg.met)
    data(ko.ids)
    data(rn.list)
    data(gene.idtype.list)
    data(gene.idtype.bods)
    data(cpd.simtypes)

### Format

cpd.accs is a data frame with 30054 observations on the following 4 variables. cpd.names is a data frame with 12314 observations on the following 5 variables. kegg.met is a character matrix of 694 rows and 3 columns. ko.ids is a character vector 8511 KEGG ortholog gene IDs, as used in KEGG ortholog pathways. rn.list is a namedlist of 21 vectors. Each vector records the row numbers for one of 21 dfferent compound ID types in cpd.accs data.frame. gene.idtype.list is a character vector of 13 common gene, transcript or protein ID types. Note some ID types are species specific, for example TAIR or ORF. gene.idtype.bods is a list of character vectors ofcommon gene, transcript or protein ID types for the 19 major research species in bods. Each element corresponds to a species. cpd.simtypes is a character vector of 7 common compound related ID types, each of them has over 1000 unique entries. Hence these ID types are good for generating simulation compound data.

### Source

ftp://ftp.ebi.ac.uk/pub/databases/chebi/Flat_file_tab_delimited/

http://www.genome.jp/kegg-bin/get_htext?br08001.keg

### Examples

    data(cpd.accs)
    data(rn.list)
    names(rn.list)
    cpd.accs[rn.list[[1]][1:4],]
    lapply(rn.list[1:4], function(rn) cpd.accs[rn[1:4],])

    data(kegg.met)
    head(kegg.met)

[Package pathview version 1.28.1 Index]