Generate a .Rmd file containing code to perform differential expression analysis with DSS

Source: R/generateRmdCodeDiffExp.R

A function to generate code that can be run to perform differential expression analysis of RNAseq data (comparing two conditions) using the DSS package. The code is written to a .Rmd file. This function is generally not called by the user, the main interface for performing differential expression analysis is the runDiffExp function.

DSS.createRmd(data.path, result.path, codefile, norm.method, disp.trend)

Arguments

data.path

The path to a .rds file containing the compData object that will be used for the differential expression analysis.

result.path

The path to the file where the result object will be saved.

codefile

The path to the file where the code will be written.

norm.method

The between-sample normalization method used to compensate for varying library sizes and composition in the differential expression analysis. Possible values are "quantile", "total" and "median".

disp.trend

A logical parameter indicating whether or not to include a trend in the dispersion estimation.

Details

For more information about the methods and the interpretation of the parameters, see the DSS package and the corresponding publications.

References

Wu H, Wang C and Wu Z (2013): A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics 14(2), 232-243

Author

Charlotte Soneson

Examples

try(
if (require(DSS)) {
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 = "DSS",
           Rmdfunction = "DSS.createRmd",
           output.directory = tmpdir, norm.method = "quantile",
           disp.trend = TRUE)
})
#> Loading required package: DSS
#> Loading required package: BiocParallel
#> Loading required package: bsseq
#> Loading required package: parallel
#> 
#> 
#> processing file: /private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpDwlx4a/tempcode21d034886f6f.Rmd
#> 1/2                  
#> 2/2 [unnamed-chunk-1]
#> output file: /private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpDwlx4a/tempcode21d034886f6f.md
#> [1] TRUE