smokingGunFinder: Find doppelgangers based on "smoking gun" phenotypes - those...

In waldronlab/doppelgangR: Identify likely duplicate samples from genomic or meta-data

Find doppelgangers based on "smoking gun" phenotypes - those that should be unique to each patient.

Description

Checks all pairwise combinations of samples for values of the "smoking" gun phenotypes that are identical.

Usage

smokingGunFinder(eset.pair, smokingguns, transFun = I, separator = ":")

Arguments

eset.pair	a list of ExpressionSets, with two elements. If the two elements are identical, the function will check for duplicate IDs within one element. If not identical, it will check for duplicate IDs between elements.
smokingguns	phenoData column names found in multiple elements of eset.pair that may contain "smoking guns" such as identifiers that should be unique to each sample.
transFun	a function to apply to IDs before comparing. By default apply no transformation.
separator	Separator between dataset name and sample name. Dataset names are added to sample names to keep track of dataset of origin.

Value

Returns an adjacency matrix for samples where matches have value 1, non-matches have value zero. Value for a sample against itself is NA.

Author(s)

Levi Waldron, Markus Riester, Marcel Ramos

Examples

example("phenoFinder")

smokingGunFinder(esets2, "days_to_death")

waldronlab/doppelgangR documentation built on Nov. 2, 2024, 11:52 p.m.