Usage
estimateHyperPar( outFile, conditions=NULL, paramsInFile=NULL, meanFile=NULL, force=TRUE, exThreshold=NULL, lambda0=NULL, paramsAllFile=NULL, smoothOnly=NULL, lowess_f=NULL, lowess_steps=NULL, verbose=NULL, veryVerbose=NULL, norm=NULL, seed=NULL, pretend=FALSE )
Arguments
outFile
Name of the output file.
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).
paramsInFile
File produced by previous run of the function using paramsAllFile flag.
meanFile
Name of the file containing joint mean and variance.
exThreshold
Threshold of lowest expression for which the estimation is done.
paramsAllFile
Name of the file to which to store all parameter values generated prior to lowess smoothing(good for later, more careful re-smoothing.)
smoothOnly
Input file contains previously sampled hyperparameters which should smoothed only.
force
Force smoothing hyperparameters, otherwise program might not produce parameters file at the end.
lambda0
Model parameter lambda0.
lowess_f
Parameter F for lowess smoothing specifying amount of smoothing.
lowess_steps
Parameter Nsteps for lowess smoothing specifying number of iterations.
veryVerbose
More verbose output.
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.