Generate HTML file(s) containing code used to run differential expression analysis.
A function to extract the code used to generate differential expression results from saved
compData result objects (typically obtained by
runDiffExp), and to write the code to HTML files. This requires that the code was saved as a character string in R markdown format in the
code slot of the result object, which is done automatically by
runDiffExp. If the differential expression analysis was performed with functions outside
compcodeR, the code has to be added manually to the result object.
A vector with paths to one or several
The path to the directory where the code HTML files will be saved.
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tmpdir <- normalizePath(tempdir(), winslash = "/") mydata.obj <- generateSyntheticData(dataset = "mydata", n.vars = 1000, samples.per.cond = 5, n.diffexp = 100, output.file = file.path(tmpdir, "mydata.rds")) runDiffExp(data.file = file.path(tmpdir, "mydata.rds"), result.extent = "voom.limma", Rmdfunction = "voom.limma.createRmd", output.directory = tmpdir, norm.method = "TMM") generateCodeHTMLs(file.path(tmpdir, "mydata_voom.limma.rds"), tmpdir)