compcodeR (version 1.8.2)

SAMseq.createRmd: Generate a .Rmd file containing code to perform differential expression analysis with SAMseq

Description

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

SAMseq.createRmd(data.path, result.path, codefile)

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.

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 SAMseq package and the corresponding publications.

References

Li J and Tibshirani R (2011): Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Statistical Methods in Medical Research

Examples

try(
if (require(samr)) {
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 = "SAMseq",
           Rmdfunction = "SAMseq.createRmd",
           output.directory = tmpdir)
})