runDiffExp {compcodeR} | R Documentation

## The main function to run differential expression analysis

### 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

    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

    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 = "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)

[Package compcodeR version 1.23.2 Index]