estimateHyperPar {BitSeq} | R Documentation |
Estimate hyperparameters for the Differential Expression model using expression samples and produced smoothed values of the hyperparameters depending on joint mean expression.
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 )
outFile |
Name of the output file. |
conditions |
|
paramsInFile |
File produced by previous run of the function using |
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. |
verbose |
Verbose output. |
Advanced options:
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. |
.par |
file containing the smoothed hyperparameters |
.ALLpar |
file containing all hyperparameter samples prior to smoothing - optional |
Peter Glaus
## Not run: cond1Files = c("data-c0b0.rpkm","data-c0b1.rpkm") cond2Files = c("data-c1b0.rpkm","data-c1b1.rpkm") estimateHyperPar( conditions=list(cond1Files, cond2Files), outFile="data.par", meanFile="data.means", verbose=TRUE) estimateHyperPar( conditions=list(cond1Files, cond2Files), outFile="data.par", meanFile="data.means", paramsFile="data.ALLpar", force=FALSE) estimateHyperPar( outFile="data.par", paramsInFile="data.ALLpar", smoothOnly=TRUE ) ## End(Not run)