hpoPlot (version 1.0)

get.cohort.information: Get Information Content Of Terms

Description

Get information content (i.e. - log frequency) of term with respect to a given cohort of patients/term-sets.

Usage

get.cohort.information(hpo.terms, patient.hpo.terms, patch.missing = FALSE)

Arguments

hpo.terms

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

patient.hpo.terms

List of HPO term sets.

patch.missing

Return an information content for all HPO terms (i.e. including those not present in the cohort) and set it to the highest information content.

Value

• Numeric vector of information contents, named by term.

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" 
	)

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

	cohort.information <- get.cohort.information(hpo.terms, patient.hpo.terms)