\name{outlierFunctions}
\alias{outlierFunctions}
\alias{proportion.outliers.robust}
\alias{proportion.outliers.mle}
\alias{qoutlier}
\alias{outlier.norm}
\alias{outlier.t}
\alias{outlier.cutoff}

\title{outliers detection functions}
\description{
Distribution based outlier detection functions.
}
\usage{
proportion.outliers.robust(x, alpha = 0.01,isUpper=TRUE,isLower=TRUE)
proportion.outliers.mle(x, alpha = 0.01,isUpper=TRUE,isLower=TRUE)
qoutlier(x, alpha = 1.5,isUpper=TRUE,isLower=TRUE,plot=FALSE,...) 
outlier.norm(x,alpha = 0.01,z.cutoff=NULL,isUpper=TRUE,isLower=TRUE,plot=FALSE) 
outlier.t(x,alpha = 0.01,z.cutoff=NULL,isUpper=TRUE,isLower=TRUE,plot=FALSE) 
outlier.cutoff(x,lBound=NULL,uBound=NULL)

}
\arguments{

	\item{x}{An integer/numeric vector used as the input}
	
	\item{alpha,z.cutoff}{alpha is the percentage of the standard deviation from the center of the data.
						  z.cutoff is the standardized z-score value. They are used as the distribution based thresholds. }
	
	\item{lBound,uBound}{Numeric scalars used as cutoff threshold for either lower limit or upper limit}			

	\item{isUpper,isLower}{logical scalars indicating whether the outliers are checked at upper or lower side of the distribution.}
	
	\item{plot}{logical scalar indicating whether to visualize the outlier detection results.}
	
	\item{...}{ other arguments to be passed to qoutlier function,currently it is ignored.}
}
\details{
qoutlier is IQR based outlier detection.
outlier.norm is based on normal distribution using Huber M-estimator of location with MAD scale 
outlier.t is based on t-distribution.
outlier.cutoff is a simple cutoff-based outlier detection.
These different outlier detection functions are used together with qaCheck method to perform outlier checks.
}

\value{
a logical vector with the same length of input vector,indicating whether each entry of the input is a outlier.
}
\author{
Mike Jiang,Greg Finak

Maintainer: Mike Jiang <wjiang2@fhcrc.org>
}

\seealso{
\code{\link{qaCheck}},\code{\link[QUALIFIER:qaReport]{qaReport}}
}



\keyword{functions}