runDiffExp {compcodeR} | R Documentation |
The main function for running differential expression analysis (comparing two conditions), using one of the methods interfaced through compcodeR
or a user-defined method.
runDiffExp(data.file, result.extent, Rmdfunction, output.directory = ".", norm.path = TRUE, ...)
data.file |
The path to a |
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 |
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 |
Charlotte Soneson
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)