geNetClassifier (version 1.12.0)

querySummary: 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.

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)