estimateHyperPar: Estimate hyperparameters for DE model using expression...

In BitSeq: Transcript expression inference and differential expression analysis for RNA-seq data

Description

Estimate hyperparameters for the Differential Expression model using expression samples and produced smoothed values of the hyperparameters depending on joint mean expression.

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.
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.

Value

.par	file containing the smoothed hyperparameters
.ALLpar	file containing all hyperparameter samples prior to smoothing - optional

Author(s)

Peter Glaus

See Also

estimateDE

Examples

## 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)

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.