A GUI to the main function for running the performance comparison between differential expression methods.
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
A list of directories containing the result files (
The directory where the results should be written. The subdirectory structure will be created automatically. If the directory already exists, it will be overwritten.
A logical parameter indicating whether or not the search should be extended recursively to subfolders of the
The width of the figures in the final report. Will be passed on to
Lists that can be used to manually set upper and lower limits for boxplots of fdr, tpr, auc, mcc, fracsign, nbrtpfp, nbrsign and typeIerror.
This function requires that the
rpanel package is installed. If this package can not be installed, please use the
runComparison function directly.
The function will create a comparison report, named compcodeR_report<timestamp>.html, in the
output.directory. It will also create subfolders named
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.
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## 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)