kNNinterface {ClassifyR} | R Documentation

## An Interface for class Package's knn Function

### Description

More details of k Nearest Neighbours are available in the documentation of `knn`.

### Usage

      ## S4 method for signature 'matrix'
    kNNinterface(measurements, classes, test, ...)
      ## S4 method for signature 'DataFrame'
    kNNinterface(measurements, classes, test, ..., verbose = 3)
      ## S4 method for signature 'MultiAssayExperiment'
    kNNinterface(measurements, test, targets = names(measurements), ...)

### 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.
`test` | An object of the same class as `measurements` with no samples in common with `measurements` and the same number of features as it.
`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 or parameters that `knn` can accept.
`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

Data tables which consist entirely of non-numeric data cannot be analysed. 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

A factor vector, the same as is returned by `knn`.

### Author(s)

Dario Strbenac

### Examples

      if(require(class))
      {
        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)
      }

      kNNinterface(measurements[, 1:9], classes[1:9], measurements[, 10, drop = FALSE])

[Package ClassifyR version 2.4.4 Index]