compcodeR (version 1.8.2)

vst.ttest.createRmd: Generate a .Rmd file containing code to perform differential expression analysis with a t-test after the variance-stabilizing transformation provided in DESeq

Description

A function to generate code that can be run to perform differential expression analysis of RNAseq data (comparing two conditions) by applying the variance-stabilizing transformation of the DESeq package followed by differential expression analysis using a t-test. 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

vst.ttest.createRmd(data.path, result.path, codefile, fit.type)

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.

fit.type

The fitting method used to get the dispersion-mean relationship. Possible values are "parametric" and "local".

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.

Details

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

References

Anders S and Huber W (2010): Differential expression analysis for sequence count data. Genome Biology 11:R106

Examples

try(
if (require(DESeq) && require(genefilter)) {
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 = "vst.ttest",
           Rmdfunction = "vst.ttest.createRmd",
           output.directory = tmpdir, fit.type = "parametric")
})