runComparisonGUI {compcodeR} | R Documentation

## A GUI to the main function for running the performance comparison between differential expression methods.

### Description

This function provides a GUI to the main function for performing comparisons among differential expression methods and generating a report in HTML format (`runComparison`). It is assumed that all differential expression results have been generated in advance (using e.g. the function `runDiffExp`) and that the result `compData` object for each data set and each differential expression method is saved separately in files with the extension `.rds`. The function opens a graphical user interface where the user can set parameter values and choose the files to be used as the basis of the comparison. It is, however, possible to circumvent the GUI and call the comparison function `runComparison` directly.

### Usage

    runComparisonGUI(
      input.directories,
      output.directory,
      recursive,
      out.width = NULL,
      upper.limits = NULL,
      lower.limits = NULL
    )

### Arguments

`input.directories` | A list of directories containing the result files (`*.rds`). All results in the provided directories will be available for inclusion in the comparison, and the selection is performed through a graphical user interface. All result objects saved in the files should be of the `compData` class, although list objects created by earlier versions of `compcodeR` are supported.
`output.directory` | The directory where the results should be written. The subdirectory structure will be created automatically. If the directory already exists, it will be overwritten.
`recursive` | A logical parameter indicating whether or not the search should be extended recursively to subfolders of the `input.directories`.
`out.width` | The width of the figures in the final report. Will be passed on to `knitr` when the HTML is generated. Can be for example "800px" (see `knitr` documentation for more information)
`upper.limits, lower.limits` | Lists that can be used to manually set upper and lower limits for boxplots of fdr, tpr, auc, mcc, fracsign, nbrtpfp, nbrsign and typeIerror.

### Details

This function requires that the `rpanel` package is installed. If this package can not be installed, please use the `runComparison` function directly.

### Value

The function will create a comparison report, named compcodeR_report<timestamp>.html, in the `output.directory`. It will also create subfolders named `compcodeR_code` and `compcodeR_figure`, where the code used to perform the differential expression analysis and the figures contained in the report, respectively, will be saved. Note that if these directories already exist they will be overwritten.

### Author(s)

Charlotte Soneson

### Examples

    ## Not run:
    mydata.obj <- generateSyntheticData(dataset = "mydata", n.vars = 12500,
                                        samples.per.cond = 5, n.diffexp = 1250,
                                        output.file = "mydata.rds")
    runDiffExp(data.file = "mydata.rds", result.extent = "voom.limma",
               Rmdfunction = "voom.limma.createRmd", output.directory = ".",
               norm.method = "TMM")
    runDiffExp(data.file = "mydata.rds", result.extent = "ttest",
               Rmdfunction = "ttest.createRmd", output.directory = ".",
               norm.method = "TMM")
    runComparisonGUI(input.directories = ".", output.directory = ".", recursive = FALSE)

    ## End(Not run)

[Package compcodeR version 1.23.2 Index]