pgb_liv\php_ms\Statistic\FalseDiscoveryRate

Class for calculating False Discovery Rate (FDR) from a object scores

Synopsis

class FalseDiscoveryRate {
}

Coverage

Methods 9.09% 1 / 11
Lines 0% 0 / 83

Violations

PHPMessDetector

Line Rule Message
219 - 227 ElseExpression The method isDecoy uses an else expression. Else is never necessary and you can simplify the code to work without else.

Members

private

  • $discoveryCount
  • $falseDiscoveryRates
  • $falsePositives
  • $fdrKey
  • $fdrTable

Methods

private

  • isDecoy() — Identifies whether the identification is a decoy or not.

public

  • calculate() — Alias of getFdrAll
  • getFalseDiscoryRates() — Gets the array of FDR rates, FDR => Score
  • getFdr() — Gets the FDR for the specified identification.
  • getFdrAll() — Calculates the FDR of all identifications, and stores them depending on options used for this instance.
  • getFdrScore() — Gets the FDR for the specified score
  • getMatches() — Gets the number of matches for the target FDR
  • getScore() — Gets the score that corresponds to the target FDR
  • reset() — Resets the cummulative FDR tallies for this instance.
  • setFdrKey() — Sets the key that should be used to record the FDR as an identification score element.
  • setFdrTableUsage() — Sets whether the FDR table is available, used by getScore/getMatches.

History