ScoreAssessmentResults: Score Gene Assessment Results

In AssessORF: Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Description

Scores the results from the assessment of a set of genes using one of three modes

Usage

ScoreAssessmentResults(x, mode = "a")

Arguments

x	An object of class Assessment and subclass Results.
mode	Must either be "a" (use all evidence), "p" (use proteomics evidence only), or "c" (use evolutionary conservation evidence only)

Details

ScoreAssessmentResults calculates an accuracy-like score for the categorization of genes within the given Results object using the given mode of calculation. The score for a mode is equal to the number of genes that were categorized to be correct for that mode divided by the total number of genes that could have been categorized as correct for that mode (i.e. a count of the number of genes that had available and useable evidence for that particular mode).

Open reading frames with proteomics evidence but no predicted start are included in the total gene count when calculating the accuracy-like score for the proteomics mode and for the all evidence mode.

Value

A numeric vector of length one containing the calculated accuracy-like score.

See Also

Assessment-class

Examples

currResObj <- readRDS(system.file("extdata",
                                  "MGAS5005_PreSaved_ResultsObj_Prodigal.rds",
                                  package = "AssessORF"))

ScoreAssessmentResults(currResObj, "a")

ScoreAssessmentResults(currResObj, "c")

ScoreAssessmentResults(currResObj, "p")

AssessORF documentation built on Nov. 8, 2020, 4:52 p.m.