kegg_pathway_download: Download one KEGG pathway

In saezlab/OmnipathR: OmniPath web service client and more

Download one KEGG pathway

Description

Downloads one pathway diagram from the KEGG Pathways database in KGML format and processes the XML to extract the interactions.

Usage

kegg_pathway_download(
  pathway_id,
  process = TRUE,
  max_expansion = NULL,
  simplify = FALSE
)

Arguments

pathway_id	Character: a KEGG pathway identifier, for example "hsa04350".
process	Logical: process the data or return it in raw format. processing means joining the entries and relations into a single data frame and adding UniProt IDs.
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 if process is TRUE, otherwise a list with two data frames: "entries" is a raw table of the entries while "relations" is a table of relations extracted from the KGML file.

See Also

• kegg_process

• kegg_pathways_download

• kegg_pathway_list

Examples

tgf_pathway <- kegg_pathway_download('hsa04350')
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>

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