edgeR.GLMQL.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 edgeR package.

Usage

edgeR.GLMQL.createRmd(data.path, result.path, codefile,
  norm.method = "TMM", disp.estimation = "CoxReid")

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	A Character parameter for calcNormFactors function. Possible values are "TMM", "TMMwzp", "RLE", "upperquartile", or "none".
disp.estimation	A Character parameter for estimateGLMCommonDisp function. Possible values are "CoxReid", "Pearson" or "deviance".

Details

For more information about the methods and the interpretation of the parameters, see the edgeR 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

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

Lun, ATL, Chen, Y, and Smyth, GK (2016). It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. Methods in Molecular Biology 1418, 391–416.

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 = "edgeR.GLMQL",
           Rmdfunction = "edgeR.GLMQL.createRmd",
           output.directory = tmpdir)

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