EBSeq.createRmd {compcodeR} | R Documentation

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

### Description

A function to generate code that can be run to perform differential expression analysis of RNAseq data (comparing two conditions) using the `EBSeq` 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

    EBSeq.createRmd(data.path, result.path, codefile, norm.method)

### 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 `"median"` and `"quantile"`.

### Details

For more information about the methods and the meaning of the parameters, see the `EBSeq` package and the corresponding publications.

### Value

The function generates a .Rmd file containing the differential expression code. This file can be executed using e.g. the `knitr` package.

### Author(s)

Charlotte Soneson

### References

Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BMG, Haag JD, Gould MN, Stewart RM and Kendziorski C (2013): EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics

### Examples

    try(
    if (require(EBSeq)) {
    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 = "EBSeq",
               Rmdfunction = "EBSeq.createRmd",
               output.directory = tmpdir, norm.method = "median")
    }
    )

[Package compcodeR version 1.23.2 Index]