DLDAinterface: An Interface for sparsediscrim Package's dlda Function

In ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Description

DLDAtrainInterface generates a trained diagonal LDA classifier and DLDApredictInterface uses it to make predictions on a test data set.

Usage

  ## S4 method for signature 'matrix'
DLDAtrainInterface(measurements, classes, ...)
  ## S4 method for signature 'DataFrame'
DLDAtrainInterface(measurements, classes, verbose = 3)
  ## S4 method for signature 'MultiAssayExperiment'
DLDAtrainInterface(measurements, targets = names(measurements), ...)
  ## S4 method for signature 'dlda,matrix'
DLDApredictInterface(model, test, ...)
  ## S4 method for signature 'dlda,DataFrame'
DLDApredictInterface(model, test, returnType = c("class", "score", "both"),
                                  verbose = 3)
  ## S4 method for signature 'dlda,MultiAssayExperiment'
DLDApredictInterface(model, test, targets = names(test), ...)  

Arguments

measurements	Either a matrix, DataFrame or MultiAssayExperiment containing the training data. For a matrix, the rows are features, and the columns are samples. If of type DataFrame, the data set is subset to only those features of type integer.
classes	Either a vector of class labels of class factor of the same length as the number of samples in measurements or if the measurements are of class DataFrame a character vector of length 1 containing the column name in measurement is also permitted. Not used if measurements is a MultiAssayExperiment object.
model	A fitted model as returned by DLDAtrainInterface.
test	An object of the same class as measurements with no samples in common with measurements and the same number of features as it. Also, if a DataFrame, the class column must be absent.
targets	If measurements is a MultiAssayExperiment, the names of the data tables to be used. "clinical" is also a valid value and specifies that integer variables from the clinical data table will be used.
...	Variables not used by the matrix nor the MultiAssayExperiment method which are passed into and used by the DataFrame method (e.g. verbose).
returnType	Default: "class". Either "class", "score" or "both". Sets the return value from the prediction to either a vector of class labels, matrix of scores for each class, or both labels and scores in a data.frame.
verbose	Default: 3. A number between 0 and 3 for the amount of progress messages to give. This function only prints progress messages if the value is 3.

Details

If measurements is an object of class MultiAssayExperiment, the factor of sample classes must be stored in the DataFrame accessible by the colData function with column name "class".

Value

For DLDAtrainInterface, a trained DLDA classifier. For DLDApredictInterface, either a factor vector of predicted classes, a matrix of scores for each class, or a table of both the class labels and class scores, depending on the setting of returnType.

Author(s)

Dario Strbenac

Examples

  # if(require(sparsediscrim)) Package currently removed from CRAN.
  #{
    # Genes 76 to 100 have differential expression.
    genesMatrix <- sapply(1:25, function(sample) c(rnorm(100, 9, 2)))
    genesMatrix <- cbind(genesMatrix, sapply(1:25, function(sample)
                                      c(rnorm(75, 9, 2), rnorm(25, 14, 2))))
    classes <- factor(rep(c("Poor", "Good"), each = 25))
    colnames(genesMatrix) <- paste("Sample", 1:ncol(genesMatrix))
    rownames(genesMatrix) <- paste("Gene", 1:nrow(genesMatrix))
    selected <- rownames(genesMatrix)[91:100]
    trainingSamples <- c(1:20, 26:45)
    testingSamples <- c(21:25, 46:50)
    
    classifier <- DLDAtrainInterface(genesMatrix[selected, trainingSamples],
                                     classes[trainingSamples])
    DLDApredictInterface(classifier, genesMatrix[selected, testingSamples])
  #}

ClassifyR documentation built on Nov. 8, 2020, 6:53 p.m.