kegg_pathways_download {OmnipathR} | R Documentation

## 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

    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>

[Package OmnipathR version 3.0.0 Index]