runDiffExp: The main function to run differential expression analysis

Description Usage Arguments Author(s) Examples

Description

The main function for running differential expression analysis (comparing two conditions), using one of the methods interfaced through compcodeR or a user-defined method.

Usage

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runDiffExp(data.file, result.extent, Rmdfunction, output.directory = ".",
  norm.path = TRUE, ...)

Arguments

data.file

The path to a .rds file containing the data on which the differential expression analysis will be performed, for example a compData object returned from generateSyntheticData.

result.extent

The extension that will be added to the data file name in order to construct the result file name. This can be for example the differential expression method together with a version number.

Rmdfunction

A function that creates an Rmd file containing the code that should be run to perform the differential expression analysis. All functions available through compcodeR can be listed using the listcreateRmd function.

output.directory

The directory in which the result object will be saved.

norm.path

Logical, whether to include the full (absolute) path to the output object in the saved code.

...

Additional arguments that will be passed to the Rmdfunction, such as parameter choices for the differential expression method.

Author(s)

Charlotte Soneson

Examples

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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"))
listcreateRmd()
runDiffExp(data.file = file.path(tmpdir, "mydata.rds"), result.extent = "voom.limma",
           Rmdfunction = "voom.limma.createRmd",
           output.directory = tmpdir, norm.method = "TMM")

## Not run: 
## The following list covers the currently available
differential expression methods:
runDiffExp(data.file = "mydata.rds", result.extent = "baySeq",
           Rmdfunction = "baySeq.createRmd",
           output.directory = ".", norm.method = "edgeR",
           equaldisp = TRUE)
runDiffExp(data.file = "mydata.rds", result.extent = "DESeq.GLM",
           Rmdfunction = "DESeq.GLM.createRmd",
           output.directory = ".", sharing.mode = "maximum",
           disp.method = "pooled", fit.type = "parametric")
runDiffExp(data.file = "mydata.rds", result.extent = "DESeq.nbinom",
           Rmdfunction = "DESeq.nbinom.createRmd",
           output.directory = ".", sharing.mode = "maximum",
           disp.method = "pooled", fit.type = "parametric")
runDiffExp(data.file = "mydata.rds", result.extent = "DESeq2",
           Rmdfunction = "DESeq2.createRmd",
           output.directory = ".", fit.type = "parametric",
           test = "Wald", beta.prior = TRUE,
           independent.filtering = TRUE, cooks.cutoff = TRUE,
           impute.outliers = TRUE)
runDiffExp(data.file = "mydata.rds", result.extent = "DSS",
           Rmdfunction = "DSS.createRmd",
           output.directory = ".", norm.method = "quantile",
           disp.trend = TRUE)
runDiffExp(data.file = "mydata.rds", result.extent = "EBSeq",
           Rmdfunction = "EBSeq.createRmd",
           output.directory = ".", norm.method = "median")
runDiffExp(data.file = "mydata.rds", result.extent = "edgeR.exact",
           Rmdfunction = "edgeR.exact.createRmd",
           output.directory = ".", norm.method = "TMM",
           trend.method = "movingave", disp.type = "tagwise")
runDiffExp(data.file = "mydata.rds", result.extent = "edgeR.GLM",
           Rmdfunction = "edgeR.GLM.createRmd",
           output.directory = ".", norm.method = "TMM",
           disp.type = "tagwise", disp.method = "CoxReid",
           trended = TRUE)
runDiffExp(data.file = "mydata.rds", result.extent = "logcpm.limma",
           Rmdfunction = "logcpm.limma.createRmd",
           output.directory = ".", norm.method = "TMM")
runDiffExp(data.file = "mydata.rds", result.extent = "NBPSeq",
           Rmdfunction = "NBPSeq.createRmd",
           output.directory = ".", norm.method = "TMM",
           disp.method = "NBP")
runDiffExp(data.file = "mydata.rds", result.extent = "NOISeq",
           Rmdfunction = "NOISeq.prenorm.createRmd",
           output.directory = ".", norm.method = "TMM")
runDiffExp(data.file = "mydata.rds", result.extent = "SAMseq",
           Rmdfunction = "SAMseq.createRmd",
           output.directory = ".")
runDiffExp(data.file = "mydata.rds", result.extent = "sqrtcpm.limma",
           Rmdfunction = "sqrtcpm.limma.createRmd",
           output.directory = ".", norm.method = "TMM")
runDiffExp(data.file = "mydata.rds", result.extent = "TCC",
           Rmdfunction = "TCC.createRmd",
           output.directory = ".", norm.method = "tmm",
           test.method = "edger", iteration = 3,
           normFDR = 0.1, floorPDEG = 0.05)
runDiffExp(data.file = "mydata.rds", result.extent = "ttest",
           Rmdfunction = "ttest.createRmd",
           output.directory = ".", norm.method = "TMM")
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 = "voom.ttest",
           Rmdfunction = "voom.ttest.createRmd",
           output.directory = ".", norm.method = "TMM")
runDiffExp(data.file = "mydata.rds", result.extent = "vst.limma",
           Rmdfunction = "vst.limma.createRmd",
           output.directory = ".", fit.type = "parametric")
runDiffExp(data.file = "mydata.rds", result.extent = "vst.ttest",
           Rmdfunction = "vst.ttest.createRmd",
           output.directory = ".", fit.type = "parametric")

## End(Not run)


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