PoissonSeq.createRmd: Generate a '.Rmd' file containing code to perform...

In unistbig/compareDEtools: Comparison of multiple DE analysis methods in R

Description

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

PoissonSeq.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.

Details

For more information about the methods and the interpretation of the parameters, see the PoissonSeq package 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)

BuKyung Baik

References

Li J, Witten DM, Johnstone I, Tibshirani R (2012). Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3): 523-38.

Examples

tmpdir <- normalizePath(tempdir(), winslash = "/")
SyntheticDataSimulation(simul.data= 'KIRC', dataset = file.path(tmpdir, "mydata.rds"), n.var = 500,
                                    samples.per.cond = 3, n.diffexp = 100, dispType='same', mode='D',
                                    fraction.upregulated=0.5, dataset.parameters=generateDatasetParameter())
compcodeR::runDiffExp(data.file = file.path(tmpdir, "mydata.rds"), result.extent = "PoissonSeq",
           Rmdfunction = "PoissonSeq.createRmd",
           output.directory = tmpdir)

unistbig/compareDEtools documentation built on May 1, 2020, 9:41 p.m.