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

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

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

Description

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

TCC.createRmd(
  data.path,
  result.path,
  codefile,
  norm.method,
  test.method,
  iteration = 3,
  normFDR = 0.1,
  floorPDEG = 0.05
)

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 "tmm", and "deseq".
test.method	The method used in TCC to find differentially expressed genes. Possible values are "edger", "deseq" and "bayseq".
iteration	The number of iterations used to find the normalization factors. Default value is 3.
normFDR	The FDR cutoff for calling differentially expressed genes in the computation of the normalization factors. Default value is 0.1.
floorPDEG	The minimum value to be eliminated as potential differentially expressed genes before performing step 3 in the TCC algorithm. Default value is 0.05.

Details

For more information about the methods and the interpretation of the parameters, see the TCC package and the corresponding publications.

Author(s)

Charlotte Soneson

References

Kadota K, Nishiyama T, and Shimizu K. A normalization strategy for comparing tag count data. Algorithms Mol Biol. 7:5, 2012.

Sun J, Nishiyama T, Shimizu K, and Kadota K. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics 14:219, 2013.

Examples

try(
if (require(TCC)) {
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 = "TCC",
           Rmdfunction = "TCC.createRmd",
           output.directory = tmpdir, norm.method = "tmm",
           test.method = "edger")
})

csoneson/compcodeR documentation built on Nov. 3, 2024, 6:05 a.m.