DSS.createRmd {compcodeR} | R Documentation

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

### Description

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.

### Usage

    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.

### Author(s)

Charlotte Soneson

### 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

### 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)
    })

[Package compcodeR version 1.20.1 Index]