find_all_subs: Find all sub IDs of an ID in a network

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Find all sub IDs of an ID in a network

Description

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.

Usage

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.

Value

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

protti documentation built on Oct. 22, 2024, 1:06 a.m.