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

In compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Description

A function to generate code that can be run to perform differential expression analysis of RNAseq data (comparing two conditions) by applying the voom transformation (from the limma package) followed by differential expression analysis with limma. 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

voom.limma.createRmd(data.path, result.path, codefile, norm.method)

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. The normalization factors are calculated using the calcNormFactors of the edgeR package. Possible values are "TMM", "RLE", "upperquartile" and "none"

Details

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

Charlotte Soneson

References

Smyth GK (2005): Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397-420

Law CW, Chen Y, Shi W and Smyth GK (2014): voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 15, R29

Examples

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 = "voom.limma", 
           Rmdfunction = "voom.limma.createRmd", 
           output.directory = tmpdir, norm.method = "TMM")

Example output

Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Registered S3 method overwritten by 'gplots':
  method         from 
  reorder.factor gdata
Warning messages:
1: no DISPLAY variable so Tk is not available 
2: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’ 


processing file: tempcode.Rmd

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  ordinary text without R code


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label: unnamed-chunk-1 (with options) 
List of 6
 $ echo   : logi TRUE
 $ eval   : logi TRUE
 $ include: logi TRUE
 $ message: logi FALSE
 $ error  : logi TRUE
 $ warning: logi TRUE

Loading required package: limma
Loading required package: edgeR

output file: tempcode.md

[1] TRUE

compcodeR documentation built on Nov. 10, 2020, 2 a.m.