Arguments
conditions
List of vectors, each vector containing names of files containing the expression samples from a replicate (Can be both technical and biological replicates. However, in order to get good results biological replicates for each condition are essential).
outPrefix
Prefix for the output files. Otherwise program creates temporary files, which are only valid for current R session.
samples
Produce samples of condition mean expression apart from PPLR and confidence.
trInfoFile
Transcript information file providing the names of transcripts.
norm
Vector of (multiplicative) normalization constants for library size normalization of expression samples. Number of constants has to match the number of expression samples files.
seed
Sets the initial random seed for repeatable experiments.
pretend
Do not execute, only print out command line calls for the C++ version of the program.