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

Source: R/generateCodeHTMLs.R

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.

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

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")
#> 
#> 
#> processing file: /private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpDwlx4a/tempcode21d061d952d2.Rmd
#> 1/2                  
#> 2/2 [unnamed-chunk-1]
#> output file: /private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpDwlx4a/tempcode21d061d952d2.md
#> [1] TRUE
generateCodeHTMLs(file.path(tmpdir, "mydata_voom.limma.rds"), tmpdir)