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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.
runComparisonGUI(input.directories, output.directory, recursive, out.width = NULL, upper.limits = NULL, lower.limits = NULL)
*.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.input.directories
.knitr
when the HTML is generated. Can be for example "800px" (see knitr
documentation for more information)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.
rpanel
package is installed. If this package can not be installed, please use the runComparison
function directly.
## 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)
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