Description Usage Arguments Value
View source: R/function.simulated.R
Loads and processes the RNAseq data before comparing it with the real foldchanges. Will produce a number of benchmarking plots and files in the current working directory.
1 | compareSimulated(ANALYSIS_NAME, txfile = "simulated.quant")
|
ANALYSIS_NAME |
A string indicating the name of the analysis/pipeline. Will be used in filenames, plot titles, etc. |
txfile |
The path to the transcript-level RNAseq expression matrix. If not given, will look for relevant files in the working directory. The expression matrix should have gene symbols in the first column/row.names, and sample names (either 's1', 's2', etc., or '1' '2', etc..) as column headers. |
qt |
A string indicating the unit of the expression matrix (either "FPKM", "TPM" or "COUNTS"). |
normMethod |
The normalization method to use (see |
uniquelyMappableLengths |
Logical, whether to use uniquely mappable length, rather than full length, for FPKM calculation. Default TRUE. |
requireAll |
logical, whether all samples are required to proceed. |
Nothing, but produces many files in the working directory...
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