TCC.createRmd {compcodeR} | R Documentation

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

### Description

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

    TCC.createRmd(
      data.path,
      result.path,
      codefile,
      norm.method,
      test.method,
      iteration = 3,
      normFDR = 0.1,
      floorPDEG = 0.05
    )

### 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 `"tmm"`, and `"deseq"`.
`test.method` | The method used in TCC to find differentially expressed genes. Possible values are `"edger"`, `"deseq"` and `"bayseq"`.
`iteration` | The number of iterations used to find the normalization factors. Default value is 3.
`normFDR` | The FDR cutoff for calling differentially expressed genes in the computation of the normalization factors. Default value is 0.1.
`floorPDEG` | The minimum value to be eliminated as potential differentially expressed genes before performing step 3 in the TCC algorithm. Default value is 0.05.

### Details

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

### Author(s)

Charlotte Soneson

### References

Kadota K, Nishiyama T, and Shimizu K. A normalization strategy for comparing tag count data. Algorithms Mol Biol. 7:5, 2012.

Sun J, Nishiyama T, Shimizu K, and Kadota K. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics 14:219, 2013.

### Examples

    try(
    if (require(TCC)) {
    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 = "TCC",
               Rmdfunction = "TCC.createRmd",
               output.directory = tmpdir, norm.method = "tmm",
               test.method = "edger")
    })

[Package compcodeR version 1.24.0 Index]