hpoPlot (version 1.0)

remove.uninformative.terms: Remove Uninformative Terms From Set

Description

Removes terms which don't add information about which terms people represented in the plot are annotated with.

Usage

remove.uninformative.terms(hpo.terms, patient.hpo.terms)

Arguments

hpo.terms

An R-Object representing the HPO, as returned by get.hpo.terms.

patient.hpo.terms

A named list of HPO term character vectors representing the phenotypes of a set of patients.

Value

• A character vector of the HPO terms which are informative in the context of the patients' phenotypes, in the sense that the frequency can't be deduced from the frequencies of its child terms alone.

Examples

data(hpo)

	patients.character.vector <- c(
		A="HP:0001382,HP:0004272,HP:0007917,HP:0004912,HP:0001596",
		B="HP:0001382,HP:0004272,HP:0002165,HP:0004800,HP:0004912",
		C="HP:0004800,HP:0001382,HP:0004912,HP:0007917,HP:0008743",
		D="HP:0001257,HP:0001382,HP:0007917,HP:0012623,HP:0002165",
		E="HP:0007917,HP:0004800,HP:0004272,HP:0001596,HP:0002165" 
	)

	patients <- term.set.list.from.character(hpo.terms, patients.character.vector)

	informative.terms <- remove.uninformative.terms(hpo.terms, patients)