runComparisonShiny: A shiny-based GUI to the main function for running the...

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

A shiny-based 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

runComparisonShiny(
  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.

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

if (interactive()) {
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")
runComparisonShiny(input.directories = ".", output.directory = ".", recursive = FALSE)
}

csoneson/compcodeR documentation built on Nov. 3, 2024, 6:05 a.m.