Download the KEGG Pathways database

Downloads all pathway diagrams in the KEGG Pathways database in KGML format and processes the XML to extract the interactions.

Usage

kegg_pathways_download(max_expansion = NULL, simplify = FALSE)

Arguments

max_expansion

Numeric: the maximum number of relations derived from a single relation record. As one entry might represent more than one molecular entities, one relation might yield a large number of relations in the processing. This happens in a combinatorial way, e.g. if the two entries represent 3 and 4 entities, that results 12 relations. If NULL, all relations will be expanded.

simplify

Logical: remove KEGG's internal identifiers and the pathway annotations, keep only unique interactions with direction and effect sign.

Value

A data frame (tibble) of interactions.

See also

• kegg_pathway_list

• kegg_process

• kegg_pathway_download

Examples

if (FALSE) {
kegg_pw <- kegg_pathways_download(simplify = TRUE)
kegg_pw
# # A tibble: 6,765 x 6
#    uniprot_source uniprot_target type  effect genesymbol_source
#    <chr>          <chr>          <chr> <chr>  <chr>
#  1 Q03113         Q15283         PPrel activ. GNA12
#  2 Q9Y4G8         P62070         PPrel activ. RAPGEF2
#  3 Q13972         P62070         PPrel activ. RASGRF1
#  4 O95267         P62070         PPrel activ. RASGRP1
#  5 P62834         P15056         PPrel activ. RAP1A
# # . with 6,760 more rows, and 1 more variable: genesymbol_target <chr>
}