Contents

0.1 Introduction

ClassifyR is a framework for cross-validated classification, with the rules for functions to be used with it explained in Section 0.11 of the introductory vignette. A fully worked example is shown how to incorporate an existing classifier from

0.2 k Nearest Neighbours

There is an implementation of the k Nearest Neighbours algorithm in the package class. Its function has the form knn(train, test, cl, k = 1, l = 0, prob = FALSE, use.all = TRUE). It accepts a matrix or a data.frame variable as input, but ClassifyR calls transformation, feature selection and classifier functions with a DataFrame, a core Bioconductor data container from S4Vectors. It also expects training data to be the first parameter, the classes of it to be the second parameter and the test data to be the third. Therefore, a wrapper for DataFrame reordering the parameters is created.

setGeneric("kNNinterface", function(measurements, ...) {standardGeneric("kNNinterface")})

setMethod("kNNinterface", "DataFrame", function(measurements, classes, test, ..., verbose = 3)
{
  splitDataset <- .splitDataAndClasses(measurements, classes)
  trainingMatrix <- as.matrix(splitDataset[["measurements"]])
  isNumeric <- sapply(measurements, is.numeric)
  measurements <- measurements[, isNumeric, drop = FALSE]
  isNumeric <- sapply(test, is.numeric)
  test <- test[, isNumeric, drop = FALSE]  
  
  if(!requireNamespace("class", quietly = TRUE))
    stop("The package 'class' could not be found. Please install it.")
  if(verbose == 3)
    message("Fitting k Nearest Neighbours classifier to data and predicting classes.")
  
  class::knn(as.matrix(measurements), as.matrix(test), classes, ...)
})

The function only emits a progress message if verbose is 3. The verbosity levels are explained in the introductory vignette. .splitDataAndClasses is an internal function in ClassifyR which ensures that classes are not in measurements. If classes is a factor vector, then the function has no effect. If classes is the character name of a column in measurements, that column is removed from the table and returned as a separate variable. The ... parameter captures any options to be passed onto knn, such as k (number of neighbours considered) and l (minimum vote for a definite decision), for example. The function is also defensive and removes any non-numeric columns from the input table.

ClassifyR also accepts a matrix and a MultiAssayExperiment as input. Provide convenience methods for these inputs which converts them into a DataFrame. In this way, only the DataFrame version of kNNinterface does the classification.

setMethod("kNNinterface", "matrix",
          function(measurements, classes, test, ...)
{
  kNNinterface(DataFrame(t(measurements), check.names = FALSE),
               classes,
               DataFrame(t(test), check.names = FALSE), ...)
})

setMethod("kNNinterface", "MultiAssayExperiment",
function(measurements, test, targets = names(measurements), ...)
{
  tablesAndClasses <- .MAEtoWideTable(measurements, targets)
  trainingTable <- tablesAndClasses[["dataTable"]]
  classes <- tablesAndClasses[["classes"]]
  testingTable <- .MAEtoWideTable(test, targets)
            
  .checkVariablesAndSame(trainingTable, testingTable)
  kNNinterface(trainingTable, classes, testingTable, ...)
})

The matrix method simply involves transposing the input matrices, which ClassifyR expects to store features in the rows and samples in the columns (customary in bioinformatics), and casting them to a DataFrame, which dispatches to the kNNinterface method for a DataFrame, which carries out the classification.

The conversion of a MultiAssayExperiment is more complicated. ClassifyR has an internal function .MAEtoWideTable which converts a MultiAssayExperiment to a wide DataFrame. targets specifies which assays to include in the conversion. By default, it can also filters the resultant table to contain only numeric variables. The internal validity function .checkVariablesAndSame checks that there is at least 1 column after filtering and that the training and testing table have the same number of variables.

0.3 Verifying the Implementation

Create a data set with 10 samples and 10 features with a clear difference between the two classes. Run leave-out-out cross-validation.

classes <- factor(rep(c("Healthy", "Disease"), each = 5), levels = c("Healthy", "Disease"))
measurements <- matrix(c(rnorm(50, 10), rnorm(50, 5)), ncol = 10)
colnames(measurements) <- paste("Sample", 1:10)
rownames(measurements) <- paste("mRNA", 1:10)

library(ClassifyR)
trainParams <- TrainParams(kNNinterface)
predictParams <- PredictParams(NULL)
classified <- runTests(measurements, classes, validation = "leaveOut", leave = 1,
                       params = list(trainParams, predictParams))
classified
## An object of class 'ClassifyResult'.
## Characteristics:
##    characteristic                value
##   Classifier Name k Nearest Neighbours
##  Cross-validation          Leave 1 Out
## Features: List of length 10 of feature identifiers.
## Predictions: List of data frames of length 1.
## Performance Measures: None calculated yet.
cbind(predictions(classified)[[1]], known = actualClasses(classified))
##       sample   class   known
## 1   Sample 1 Healthy Healthy
## 2   Sample 2 Healthy Healthy
## 3   Sample 3 Healthy Healthy
## 4   Sample 4 Healthy Healthy
## 5   Sample 5 Healthy Healthy
## 6   Sample 6 Disease Disease
## 7   Sample 7 Disease Disease
## 8   Sample 8 Disease Disease
## 9   Sample 9 Disease Disease
## 10 Sample 10 Disease Disease

NULL is specified instead of a function to PredictParams because one function does training and prediction. As expected for this easy task, the classifier predicts all samples correctly.