cpd.accs: Mapping data between compound or gene IDs and KEGG accessions

Description Usage Format Source Examples

Description

Mapping data between compound or gene IDs and KEGG accessions

Usage

1
2
3
4
5
6
7
8

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

1
2
3
4
5
6
7
8

DGendooLab/pathviewM documentation built on Dec. 17, 2021, 4 p.m.