Generate a .Rmd file containing code to perform differential expression analysis with NOISeq

Source: R/generateRmdCodeDiffExp.R

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

NOISeq.prenorm.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 function from the edgeR package. Possible values are "TMM", "RLE", "upperquartile" and "none".

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 NOISeq package and the corresponding publications.

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

Robinson MD and Oshlack A (2010): A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11:R25

Tarazona S, Furio-Tari P, Ferrer A and Conesa A (2012): NOISeq: Exploratory analysis and differential expression for RNA-seq data. R package

Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A and Conesa A (2011): Differential expression in RNA-seq: a matter of depth. Genome Res 21(12), 2213-2223

Author

Charlotte Soneson

Examples

try(
if (require(NOISeq)) {
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 = "NOISeq",
           Rmdfunction = "NOISeq.prenorm.createRmd",
           output.directory = tmpdir, norm.method = "TMM")
})
#> Loading required package: NOISeq
#> Loading required package: splines
#> Loading required package: Matrix
#> 
#> Attaching package: ‘Matrix’
#> The following object is masked from ‘package:S4Vectors’:
#> 
#>     expand
#> 
#> Attaching package: ‘NOISeq’
#> The following object is masked from ‘package:edgeR’:
#> 
#>     rpkm
#> 
#> 
#> processing file: /private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpDwlx4a/tempcode21d041731013.Rmd
#> 1/2                  
#> 2/2 [unnamed-chunk-1]
#> output file: /private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpDwlx4a/tempcode21d041731013.md
#> [1] TRUE