ScoreAssessmentResults {AssessORF} | R Documentation

## Score Gene Assessment Results

### 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), "c" (use evolutionary conservation evidence only), or "w" (use all evidence but with weights).

### 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 both all evidence modes.

In the weighted, all evidence mode, weights for each category are determined by the number of types of evidence that are supporting or against genes in the category. Counts are multiplied by their corresponding weight, and the maximum value for a weight is 2.

### 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")

[Package AssessORF version 1.0.2 Index]