mutual_exclusivity_pairwise: Determine whether two phenotypes are mutually exclusive

In xu-hong/rphenoscape: Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase

Determine whether two phenotypes are mutually exclusive

Description

Determines whether the data in the KB includes evidence for mutual exclusivity between two given phenotypes.

Usage

mutual_exclusivity_pairwise(
  phenotype.a,
  phenotype.b,
  studies = NULL,
  charstates = NULL,
  quality_opposites = NULL
)

Arguments

phenotype.a	character or phenotype object, phenotype ID (IRI) if character, or a phenotype object obtained by passing phenotype ID to as.phenotype() function.
phenotype.b	character or phenotype object, phenotype ID (IRI) if character, or a phenotype object obtained by passing phenotype ID to as.phenotype() function.
studies	character, a vector of study IDs. This is an optional parameter that acts as a filter in case the determination of mutual exclusivity is to be based only on the evidence found in a particular set of studies. The default is NULL, which means that all studies present in the KB database will be considered for evidence.
charstates	dataframe, a dataframe obtained from charstates() by passing a list of the two phenotypes as argument. This optional parameter exists to speed up the computation for the mutually_exclusive() function since mutually_exclusive() repeatedly calls mutual_exclusivity_pairwise(). The default is NULL. Note that passing this argument but doing so incorrectly can result in wrong output.
quality_opposites	dataframe, an optional dataframe containing columns "quality.a" and "quality.b" to denote pairs of phenotypic quality terms, in the form of their term IRIs, to be considered opposites of each others. See documentation under mutually_exclusive() for more details.

Details

See mutually_exclusive() for details on which links in the data are considered as strong or weak evidence for mutual exclusivity and compatibility.

Value

A character (string), the mutual exclusivity type among the two phenotypes. See mutually_exclusive() for documentation on the possible values, although note that this function returns these as a character vector, not levels of an ordered factor.

xu-hong/rphenoscape documentation built on Jan. 28, 2024, 12:22 p.m.