kegg_pathways_download {OmnipathR} | R Documentation |
Downloads all pathway diagrams in the KEGG Pathways database in KGML format and processes the XML to extract the interactions.
kegg_pathways_download(max_expansion = NULL, simplify = FALSE)
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 |
simplify |
Logical: remove KEGG's internal identifiers and the pathway annotations, keep only unique interactions with direction and effect sign. |
A data frame (tibble) of interactions.
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>