calcStats: Calc Stats

In d3b-center/medullo-classifier-package: Medulloblastoma Classifier

Calc Stats

Description

Function to calculate statistics on prediction class and actual class of a medulloblastoma dataset.

Usage

calcStats(myClassActual = NULL, myClassPred = NULL)

Arguments

myClassActual	a vector of characters corresponding to the actual classification for each sample in the dataset. The vector can only include the characters 'WNT', SHH', 'Group3', 'Group4', and 'U'.
myClassPred	a vector of characters corresponding to the prediction made for each sample. The vector can only include the characters 'WNT', SHH', 'Group3', and 'Group4'.

Details

This function can be used to analyze prediction class if the correct classification of the provided Medulloblastoma dataset is known. Function calculates an accuracy score, a confidence interval, creates a confusion matrix, and displays other useful statistics (i.e. Sensitivity, Specificity).

The input parameters are character vectors and each value in the vector corresponds to one of the four molecular subtypes of Medulloblastoma (i.e. Sonic Hedgehog (SHH), WNT, Group 3, and Group 4).

The expected output is a list of length 4. The first element in the outputted list is the confusion matrix, which is a data frame of dimension 4x4. The second element is a data frame containing overall statistics on the accuracy of the classifier. The third element in the the list is also a data frame containing class statistics (e.g. Sensitivity, Specificity, etc.). The last element in the list is a character which corresponds to the the prediction accuracy of the medulloblastoma classifier.

Author(s)

Pichai Raman

Komal S. Rathi

Sherjeel Arif

Examples

## prediction class
predictionClass <- c("Group3", "WNT", "WNT", "Group4", "SHH", "Group4")

## observed class
actualClass <- c("Group4", "WNT", "SHH", "Group4", "SHH", "Group4")

## call function to obtain accuracy and other statistics
stats <- medulloPackage::calcStats(actualClass, predictionClass)

## View the contents of stats
confusion.matrix <- stats[[1]]
overall.stats <- stats[[2]]
class.stats <- stats[[3]]
accuracy <- stats[[4]]

head(confusion.matrix)
head(overall.stats)
head(class.stats)
head(accuracy)

d3b-center/medullo-classifier-package documentation built on June 28, 2023, 8:16 p.m.