kegg_pathways_download: Download the KEGG Pathways database

In saezlab/OmnipathR: OmniPath web service client and more

Download the KEGG Pathways database

Description

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

## Not run: 
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>

## End(Not run)

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.