querySummary {geNetClassifier} | R Documentation

## Summary of the query.

### Description

Counts the number of samples assigned to each class and calculates basic statistics regarding the assignment probabilities.

### Usage

    querySummary(queryResult, showNotAssignedSamples = TRUE, numDecimals = 2,
        verbose = TRUE)

### Arguments

`queryResult` | Object returned by `queryGeNetClassifier`
`showNotAssignedSamples` | Logical. Shows the two most likely classes for the NotAssigned samples and the probabilities of belonging to each of them.
`numDecimals` | Integer. Number of decimals to show on the statistics.
`verbose` | Logical. If TRUE, messages indicating the execution progress will be printed on screen.

### Value

Returns a list with the following fields:

- callRate Count and percentage of assigned samples.

- assigned Number of samples assigned to each class and mean and SD of the assignment probabilities.

- notAssignedSamples Optional. Most likely classes for the Not Assigned samples.

### Author(s)

Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain

### See Also

Main package function and classifier training: `geNetClassifier`
Query the classifier: `queryGeNetClassifier`

### Examples

    ##########################
    ## Classifier training
    ##########################

    # Load an expressionSet:
    library(leukemiasEset)
    data(leukemiasEset)

    # Select the train samples:
    trainSamples <- c(1:10, 13:22, 25:34, 37:46, 49:58)

    # Train a classifier or load a trained one:
    # leukemiasClassifier <- geNetClassifier(leukemiasEset[,trainSamples],
    #    sampleLabels="LeukemiaType", plotsName="leukemiasClassifier")
    data(leukemiasClassifier) # Sample trained classifier

    ##########################
    ## Classifier query
    ##########################
    # Select the samples to query the classifier
    #   - Real use: samples whose class we want to known
    querySamples <- "GSM330154.CEL"
    #   - External validation: samples not used for training
    querySamples <- c(1:60)[-trainSamples]

    # Make a query to the classifier:
    queryResult <- queryGeNetClassifier(leukemiasClassifier, leukemiasEset[,querySamples])

    ##########################
    ## Query Summary
    ##########################
    # Obtain an overview of the results
    querySummary(queryResult)

[Package geNetClassifier version 1.27.9 Index]