R: The main function to run differential expression analysis

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 1.24.0 Index]