RUMIcurve {SemDist} | R Documentation

## Information accretion based predictor assessment (across many thresholds)

### Description

Reads in a (tab-delimited) file containing the true annotations for a set of sequences, a (tab-delimited) file containing the predicted annotations and corresponding scores for the same sequences. Calculates and outputs the average remaining uncertainty, misinformation, and semantic similarity at a series of user-specified thresholds.

### Usage

    RUMIcurve(ont, organism, increment = 0.05, truefile, predfiles,
              IAccr = NULL, add.weighted = FALSE,
              add.prec.rec = FALSE)

### 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.
`increment` | A numeric value between 0 and 1 indicating the distance between each threshold that should be calculated. Note that the iteration starts from a threshold of 1, so an increment value of 0.08 will result in the thresholds 0.92, 0.84, 0.76 ... being used.
`truefile` | A character vector indicating the file from which to read the true annotations for the given sequences. Should be tab-delimited, with the first column containing the sequence ids and the second containing GO accessions.
`predfiles` | A character vector containing which files to read in as the predicted annotations. Should be tab-delimited, with the first column containing sequences, the second column containing GO accessions, and the third column containing the predictors 0-1 score for that 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.
`add.weighted` | A boolean indicating whether or not to add calculation of information content weighted versions of RU, MI, and SS to the output.
`add.prec.rec` | A boolean indicating whether or not to calculate precision, recall and specificity values for the prediction at each threshold and add to the output.

### Value

Returns a named list with the same number of elements as the input "predfiles". Each element is a data frame containing all of the user-requested values for the data at each threshold.

### Author(s)

Ian Gonzalez and Wyatt Clark

### See Also

`computeIA` `findRUMI`

### Examples

    # Using test data sets from SemDist, plot a RUMI curve:
    truefile <- system.file("extdata", "MFO_LABELS_TEST.txt", package="SemDist")
    predfile <- system.file("extdata", "MFO_PREDS_TEST.txt", package="SemDist")
    avgRUMIvals <- RUMIcurve("MF", "human", 0.05, truefile, predfile)
    firstset <- avgRUMIvals[[1]]
    plot(firstset$RU, firstset$MI)

[Package SemDist version 1.20.0 Index]