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

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



A SummarizedBenchmark object.


A string with the name of the evaluation metric.


A string with an assay name. Indicates the assay that should be given as input to this performance metric.


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'.


A SummarizedBenchmark object.

See also


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) } )