querySummary: Summary of the query.

In geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles

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)

geNetClassifier documentation built on Nov. 8, 2020, 4:53 p.m.