NBPSeq.createRmd {compcodeR} | R Documentation

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

### Description

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

    NBPSeq.createRmd(data.path, result.path, codefile, norm.method,
      disp.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. The normalization factors are calculated using the `calcNormFactors` function from the `edgeR` package. Possible values are `"TMM"`, `"RLE"`, `"upperquartile"` and `"none"`.
`disp.method` | The method to use to estimate the dispersion values. Possible values are `"NBP"` and `"NB2"`.

### Details

For more information about the methods and the interpretation of the parameters, see the `NBPSeq` and `edgeR` packages and the corresponding publications.

### Value

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

### Author(s)

Charlotte Soneson

### References

Robinson MD, McCarthy DJ and Smyth GK (2010): edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140

Robinson MD and Oshlack A (2010): A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11:R25

Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq. Statistical Applications in Genetics and Molecular Biology 10(1), 1-28

### Examples

    try(
    if (require(NBPSeq)) {
    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 = "NBPSeq",
               Rmdfunction = "NBPSeq.createRmd",
               output.directory = tmpdir, norm.method = "TMM", disp.method = "NBP")
    })

[Package compcodeR version 1.20.1 Index]