ROTS.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 ROTS package.

Usage

ROTS.createRmd(data.path, result.path, codefile, normalize = TRUE,
  transformation = TRUE, B = 1000, K = NULL, log = FALSE)

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.
normalize	A logical indicating whether to run ROTS with TMM normalized count or raw count data. Default value is True (TMM normalized).
transformation	A logical indicating whether to run ROTS with voom transformation. Default value is True.
B	An integer specifying the number of bootstrap and permutation resamplings (default 1000).
K	An integer indicating the largest top list size considered. If no value is given, 1/4 of the features are used.
log	A logical parameter indicating whether input data is log2 scaled. Choices are as for the method argument of ROTS function. This information is only used to calculate log fold change.

Details

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

L. L. Elo, S. Filen, R. Lahesmaa and T. Aittokallio: Reproducibility-optimized test statistic for ranking genes in microarray studies. IEEE/ACM Transactions on Computational Biology and Bioinformatics 5: 423–431, 2008.

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 = "ROTS",
           Rmdfunction = "ROTS.createRmd", transformation=TRUE, normalize = TRUE,
           output.directory = tmpdir, B = 1000,
           K = 500, log = FALSE)

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