compareSimulated: Transcript-level benchmark of the simulated data
In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

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 `donorm`). Defaults to 'TMM'.
`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.