hpoPlot (version 1.0)

get.term.patient.matrix: Get Term By Patient Matrix

Description

Create a matrix of logicals where the patients are represented by the rows, and the HPO terms present in at least 1 patient are represented by the columns. The values in the cells are then TRUE if the patient of the row has the phenotype of the column and FALSE otherwise.

Usage

get.term.patient.matrix(patient.hpo.terms.with.ancs)

Arguments

patient.hpo.terms.with.ancs

List of HPO term character vectors, most usually containing ancestors. Such a list can be obtained from a list containing only the leaf terms using `lapply(list.of.term.sets, function(x) get.ancestors(hpo.terms, x))'.

Value

• Logical matrix

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)
	
	term.patient.matrix <- get.term.patient.matrix(
		lapply(
			patient.hpo.terms, 
			function(patient.terms) get.ancestors(hpo.terms, patient.terms)
		)
	)