edgeRselection {ClassifyR} | R Documentation

## Feature Selection Based on Differential Expression for Count Data

### Description

Performs a differential expression analysis between classes and chooses the features which have best resubstitution performance. The data may have overdispersion and this is modelled.

### Usage

      ## S4 method for signature 'matrix'
    edgeRselection(counts, classes, ...)
      ## S4 method for signature 'DataFrame'
    edgeRselection(counts, classes, datasetName,
                       normFactorsOptions = NULL, dispOptions = NULL, fitOptions = NULL,
                   trainParams, predictParams, resubstituteParams,
                   selectionName = "edgeR LRT", verbose = 3)
      ## S4 method for signature 'MultiAssayExperiment'
    edgeRselection(counts, targets = NULL, ...)

### Arguments

`counts` | Either a `matrix` or `MultiAssayExperiment` containing the unnormalised counts.
`classes` | A vector of class labels of class `factor` of the same length as the number of samples in `measurements`. Not used if `measurements` is a `MultiAssayExperiment` object.
`targets` | If `measurements` is a `MultiAssayExperiment`, the names of the data tables of counts to be used.
`...` | Variables not used by the `matrix` nor the `MultiAssayExperiment` method which are passed into and used by the `DataFrame` method.
`datasetName` | A name for the data set used. Stored in the result.
`normFactorsOptions` | A named `list` of any options to be passed to `calcNormFactors`.
`dispOptions` | A named `list` of any options to be passed to `estimateDisp`.
`fitOptions` | A named `list` of any options to be passed to `glmFit`.
`trainParams` | A container of class `TrainParams` describing the classifier to use for training.
`predictParams` | A container of class `PredictParams` describing how prediction is to be done.
`resubstituteParams` | An object of class `ResubstituteParams` describing the performance measure to consider and the numbers of top features to try for resubstitution classification.
`selectionName` | A name to identify this selection method by. Stored in the result.
`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

The differential expression analysis follows the standard `edgeR` steps of estimating library size normalisation factors, calculating dispersion, in this case robustly, and then fitting a generalised linear model followed by a likelihood ratio test.

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

An object of class `SelectResult` or a list of such objects, if the classifier which was used for determining the specified performance metric made a number of prediction varieties.

### Author(s)

Dario Strbenac

### References

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Mark D. Robinson, Davis McCarthy, and Gordon Smyth, 2010, Bioinformatics, Volume 26 Issue 1, https://academic.oup.com/bioinformatics/article/26/1/139/182458.

### Examples

      if(require(parathyroidSE) && require(PoiClaClu))
      {
        data(parathyroidGenesSE)
        expression <- assays(parathyroidGenesSE)[[1]]
        sampleNames <- paste("Sample", 1:ncol(parathyroidGenesSE))
        colnames(expression) <- sampleNames
        DPN <- which(colData(parathyroidGenesSE)[, "treatment"] == "DPN")
        control <- which(colData(parathyroidGenesSE)[, "treatment"] == "Control")
        expression <- expression[, c(control, DPN)]
        classes <- factor(rep(c("Contol", "DPN"), c(length(control), length(DPN))))
        expression <- expression[rowSums(expression > 1000) > 8, ] # Make small data set.

        selected <- edgeRselection(expression, classes, "DPN Treatment",
                       trainParams = TrainParams(classifyInterface),
                       predictParams = PredictParams(NULL),
                       resubstituteParams = ResubstituteParams(nFeatures = seq(10, 100, 10),
                                            performanceType = "balanced error", better = "lower"))

        head(selected@rankedFeatures[[1]])
        plotFeatureClasses(expression, classes, "ENSG00000044574",
                           dotBinWidth = 500, xAxisLabel = "Unnormalised Counts")
      }

[Package ClassifyR version 2.8.0 Index]