FunctionalityScore: Compute the Functionality Score for each subject fit in a...

Description Usage Arguments Value Note Examples

View source: R/Scores.R

Description

Computes the functionality score for each observation from the gamma matrix of a COMPASS model fit. The scores are normalized according to the total number of possible subsets that could be observed (2^M - 1).

Usage

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FunctionalityScore(x, n, markers = NULL)

## S3 method for class 'COMPASSResult'
FunctionalityScore(x, n, markers = NULL)

## Default S3 method:
FunctionalityScore(x, n, markers = NULL)

Arguments

x

An object of class COMPASSResult, as returned by COMPASS. Alternatively, a matrix of functionality scores, used under the assumption that the 'null' category has been dropped.

n

The number of markers included in an experiment. It is inferred from the data when x is a COMPASSResult.

markers

The set of markers for which to compute a Functionality score. By default uses all markers. Must match names returned by markers().

Value

A numeric vector of functionality scores.

Note

The null category is implicitly dropped when computing the functionality score for a COMPASS result; this is not true for the regular matrix method.

Examples

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COMPASS documentation built on Nov. 1, 2018, 5:03 a.m.