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

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Description

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

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EBSeq.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. Possible values are "median" and "quantile".

Details

For more information about the methods and the meaning of the parameters, see the EBSeq package and the corresponding publications.

Value

The function generates a .Rmd file containing the differential expression code. This file can be executed using e.g. the knitr package.

Author(s)

Charlotte Soneson

References

Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BMG, Haag JD, Gould MN, Stewart RM and Kendziorski C (2013): EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics

Examples

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try(
if (require(EBSeq)) {
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 = "EBSeq",
           Rmdfunction = "EBSeq.createRmd",
           output.directory = tmpdir, norm.method = "median")
}
)

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