kegg_process {OmnipathR} | R Documentation

## Interactions from KGML

### Description

Processes KEGG Pathways data extracted from a KGML file. Joins the entries and relations into a single data frame and translates the Gene Symbols to UniProt IDs.

### Usage

    kegg_process(entries, relations, max_expansion = NULL, simplify = FALSE)

### Arguments

`entries` | A data frames with entries extracted from a KGML file by `kegg_pathway_download`.
`relations` | A data frames with relations extracted from a KGML file by `kegg_pathway_download`.
`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. In rare cases when a pathway doesn't contain any relation, returns `NULL`.

### See Also

- `kegg_pathway_download`

- `kegg_pathways_download`

- `kegg_pathway_list`

### Examples

    hsa04350 <- kegg_pathway_download('hsa04350', process = FALSE)
    tgf_pathway <- kegg_process(hsa04350$entries, hsa04350$relations)
    tgf_pathway

    # # A tibble: 50 x 12
    #    source target type  effect arrow relation_id kegg_id_source
    #    <chr>  <chr>  <chr> <chr>  <chr> <chr>       <chr>
    #  1 51     49     PPrel activ. -->   hsa04350:1  hsa:7040 hsa:.
    #  2 57     55     PPrel activ. -->   hsa04350:2  hsa:151449 hs.
    #  3 34     32     PPrel activ. -->   hsa04350:3  hsa:3624 hsa:.
    #  4 20     17     PPrel activ. -->   hsa04350:4  hsa:4838
    #  5 60     46     PPrel activ. -->   hsa04350:5  hsa:4086 hsa:.
    # # . with 45 more rows, and 5 more variables: genesymbol_source <chr>,
    # #   uniprot_source <chr>, kegg_id_target <chr>,
    # #   genesymbol_target <chr>, uniprot_target <chr>

[Package OmnipathR version 3.0.0 Index]