Description Usage Arguments Details Author(s) References Examples
View 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 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.
1 2 3 4 5 6 7 8 9 10 | TCC.createRmd(
data.path,
result.path,
codefile,
norm.method,
test.method,
iteration = 3,
normFDR = 0.1,
floorPDEG = 0.05
)
|
data.path |
The path to a .rds file containing the |
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 |
test.method |
The method used in TCC to find differentially expressed genes. Possible values are |
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. |
For more information about the methods and the interpretation of the parameters, see the TCC
package and the corresponding publications.
Charlotte Soneson
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.
1 2 3 4 5 6 7 8 9 10 11 | 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")
})
|
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