generateCodeHTMLs {compcodeR} | R Documentation

## Generate HTML file(s) containing code used to run differential expression analysis.

### Description

A function to extract the code used to generate differential expression results from saved `compData` result objects (typically obtained by `runDiffExp`), and to write the code to HTML files. This requires that the code was saved as a character string in R markdown format in the `code` slot of the result object, which is done automatically by `runDiffExp`. If the differential expression analysis was performed with functions outside `compcodeR`, the code has to be added manually to the result object.

### Usage

    generateCodeHTMLs(input.files, output.directory)

### Arguments

`input.files` | A vector with paths to one or several `.rds` files containing `compData` objects with the results from differential expression analysis. One code HTML file is generated for each file in the vector.
`output.directory` | The path to the directory where the code HTML files will be saved.

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

[Package compcodeR version 1.20.1 Index]