find_all_subs function

Find all sub IDs of an ID in a network

For a given ID, find all sub IDs and their sub IDs etc. The type of relationship can be selected too. This is a helper function for other functions.

find_all_subs(
  data,
  ids,
  main_id = id,
  type = type,
  accepted_types = "is_a",
  exclude_parent_id = FALSE
)

Arguments

• data: a data frame that contains relational information on IDs (main_id) their sub IDs (sub_id) and their relationship (type). For ChEBI this data frame can be obtained by calling fetch_chebi(relation = TRUE). For ECO data it can be obtained by calling fetch_eco(relation = TRUE).
• ids: a character vector of IDs for which sub IDs should be searched.
• main_id: a character or integer column containing IDs. Default is id for ChEBI IDs.
• type: a character column that contains the type of interactions. Default is type for ChEBI IDs.
• accepted_types: a character vector containing the accepted_types of relationships that should be considered for the search. It is possible to use "all" relationships. The default type is "is_a". A list of possible relationships for e.g. ChEBI IDs can be found here.
• exclude_parent_id: a logical value that specifies if the parent ID should be included in the returned list.

Returns

A list of character vectors containing the provided ID and all of its sub IDs. It contains one element per input ID.