findRUMI {SemDist} | R Documentation

## Information accretion based predictor assessment

### Description

Reads in a file containing the true terms annotating a set of sequences and a file containing the predicted terms and scores for a set of sequences and outputs a data frame containing the remaining uncertainty and misinformation values for the predictions made for each sequence.

### Usage

    findRUMI(ont, organism, threshold = 0.05, truefile="",
              predfile = "", IAccr = NULL)

### Arguments

`ont` | Character representation of ontology version to use. One of "CC", "MF", or "BP" , corresponding to Cellular Component, Molecular Function, and Biological Process.
`organism` | A character vector indicating which organism(s) annotation data to use.
`threshold` | Score above which a predicted annotation should be included in the calculation. Must be a numeric value between 0 and 1, or else findRUMI throws an error.
`truefile` | Text file from which to read true annotations of sequences. Should be a tab-delineated file with 2 columns: Sequences and GO terms (accessions).
`predfile` | Text file from which to read predicted annotations of sequences. Should be a tab-delineated file with 3 columns: Sequences, GO terms (accessions), and probability score from 0 to 1 for each prediction.
`IAccr` | A variable containing a named numeric vector of IA values for all the GO terms being used that will be used for calculations instead of R packages. This argument is optional.

### Value

A data frame containing the RU and MI values for each sequence in the file.

### Author(s)

Ian Gonzalez and Wyatt Clark

### See Also

`computeIA` `RUMIcurve`

### Examples

    # Using test data sets from SemDist, calculate RU and MI:
    truefile <- system.file("extdata", "MFO_LABELS_TEST.txt", package="SemDist")
    predfile <- system.file("extdata", "MFO_PREDS_TEST.txt", package="SemDist")
    rumiTable <- findRUMI("MF", "human", 0.75, truefile, predfile)
    avgRU <- mean(rumiTable$RU)
    avgMI <- mean(rumiTable$MI)

[Package SemDist version 1.24.0 Index]