addPerformanceMetric: Add performance metric to SummarizedBenchmark object

In SummarizedBenchmark: Classes and methods for performing benchmark comparisons

Description

This is a function to define performance metrics for benchmarking methods. The function is saved into the performanceMetrics slot.

Usage

addPerformanceMetric(object, evalMetric, assay, evalFunction = NULL)

Arguments

object	A SummarizedBenchmark object.
evalMetric	A string with the name of the evaluation metric.
assay	A string with an assay name. Indicates the assay that should be given as input to this performance metric.
evalFunction	A function that calculates a performance metric. It should contain at least two arguments, query and truth, where query is the output vector of a method and truth is the vector of true values. If additional parameters are specified, they must contain default values. If NULL, the 'evalMetric' string must be the name of a predefined metric available through 'availableMetrics()$function'.

Value

A SummarizedBenchmark object.

Author(s)

Alejandro Reyes

See Also

availableMetrics, performanceMetrics

Examples

data( sb )
sb <- addPerformanceMetric(
   object=sb,
   assay="qvalue",
   evalMetric="TPR",
   evalFunction = function( query, truth, alpha=0.1 ){
       goodHits <- sum( (query < alpha) & truth == 1 )
       goodHits / sum(truth == 1)
   }
)

SummarizedBenchmark documentation built on Nov. 8, 2020, 8:30 p.m.