runSimulationAnalysis: Run Analysismethods
In unistbig/compareDEtools: Comparison of multiple DE analysis methods in R

Run Analysismethods

runSimulationAnalysis(working.dir, output.dir, real = FALSE,
  fpc = FALSE, data.types, fixedfold = FALSE, rep, nsample, nDE,
  fraction.upregulated, disp.Types, modes, AnalysisMethods,
  para = list())

`working.dir`	Input file location
`output.dir`	Result file location
`real`	A logical indicating whether this analysis is for synthetic data or real data. Possible values are TRUE or FALSE.
`fpc`	A logical indicating whether simulation data is made from a single sample group (e.g. normal) to calculate False positive counts. Possible values are TRUE or FALSE. Only used for real data analysis.
`data.types`	A vector indicating types of dataset (e.g. data.types = c(KIRC, Bottomly, mBdK and mKdB))
`fixedfold`	A logical indicating whether simulation data is made from fixed fold to imitate SEQC counts data. Possible values are TRUE or FALSE. Only applied if this simulation is synthetic data simulation.
`rep`	An integer specifying iterations each test perform.
`nsample`	A vector indicating number of samples.
`nDE`	A vector indicating number of generated DE genes in the synthetic data.
`fraction.upregulated`	A vector specifying proportion of upregulated DE genes in the synthetic data. Default value is 0.5. (e.g. fraction.upregulated = c(0.5, 0.7 and 0.9)) This vector is available only if fixed fold is FALSE.
`disp.Types`	A vector indicating how is the dispersion parameter assumed to be for each condition to make a synthetic data. Possible values are 'same' and 'different'.
`modes`	A vector specifying test conditions we used for simulation data generation. "D" for basic simulation (not adding outliers). "R" for adding 5 "OS"for adding outlier sample to each sample group. "DL" for decreasing KIRC simulation dispersion 22.5 times (similar to SEQC data dispersion) to compare with SEQC data.
`AnalysisMethods`	A vector specifying DEmethods used for the analysis. (e.g. 'edgeR','edgeR.ql','edgeR.rb','DESeq.pd','DESeq2','voom.tmm','voom.qn','voom.sw','ROTS','BaySeq','BaySeq.qn,'PoissonSeq','SAMseq')
`para`	A list parameter consists of multiple lists corresponding each method. Each method list contains multiple parameters to run each DE analysis method.