\name{parameters-class}
\Rdversion{1.1}
\docType{class}
\alias{parameters}
\alias{parameters-class}


\title{Class "parameters" }
\description{This object contains contains parameters of GADEM analysis}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("motif_gadem", ...)}.
}
\section{Slots}{
	 \describe{
   	\item{numWordGroup}{:Number of non-zero k-mer groups. }
	\item{numTop3mer}{:Number of top-ranked trimers for spaced dyads (default: 20). }
	\item{verbose}{:Print immediate results on screen [1-yes (default), 0-no].}
	\item{numTop4mer}{:Number of top-ranked tetramers for spaced dyads (default: 40).}
	\item{numTop5mer}{:Number of top-ranked pentamers for spaced dyads (default: 60).}
	\item{numGeneration}{:Number of genetic algorithm (GA) generations (default: 5).}
	\item{populationSize}{:GA population size (default: 100).}
	\item{pValue}{:P-value cutoff for declaring BINDING SITES (default: 0.0002). }
	\item{eValue}{:ln(E-value) cutoff for selecting MOTIFS (default: 0.0).}
	\item{extTrim}{:Base extension and trimming (1 -yes, 0 -no) (default: 1).}
	\item{minSpaceWidth}{:Minimal number of unspecified nucleotides in spaced dyads (default: 0).}
	\item{maxSpaceWidth}{:Maximal number of unspecified nucleotides in spaced dyads (default: 10).}
	\item{useChIPscore}{:Use top-scoring sequences for deriving PWMs.}
	\item{numEM}{:Number of EM steps (default: 40).}
	\item{fEM}{:Fraction of sequences used in EM to obtain PWMs in an unseeded analysis (default: 0.5).}
	\item{widthWt}{:For -posWt 1 or 3, width of central sequence region with large EM weights for PWM optimization (default: 50).}
	\item{fullScan}{:GADEM keeps two copies of the input sequences internally.}
	\item{slideWinPWM}{:Sliding window for comparing pwm similarity (default : 6).}
	\item{stopCriterion}{}
	\item{numBackgSets}{:Number of sets of background sequences (default: 10).}
	\item{weightType}{:Weight profile for positions on the sequence.}
	\item{bFileName}{:Reading user-specified background models.}
	\item{Spwm}{:File name for the seed PWM, when a seeded approach is used.}
	\item{nSequences}{:Number of input sequences.}
	\item{maskR}{:Mask low-complexity sequences or repeats.}
	\item{nmotifs}{:Maximal number of motifs sought.}	
  }
}

\author{Arnaud Droit \email{arnaud.droit@crchuq.ulaval.ca}}

\seealso{
	 \code{\linkS4class{gadem}} , \code{\linkS4class{align}}, \code{\linkS4class{motif}}
}
\examples{
showClass("parameters")
}
\keyword{classes}