% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/DIscBIO-generic-FindOutliers.R

\name{FindOutliers}

\alias{FindOutliers}

\alias{FindOutliers,DISCBIO-method}

\title{Inference of outlier cells}

\usage{

FindOutliers(

  object,

  K,

  outminc = 5,

  outlg = 2,

  probthr = 0.001,

  thr = 2^-(1:40),

  outdistquant = 0.75,

  plot = TRUE,

  quiet = FALSE

)

\S4method{FindOutliers}{DISCBIO}(

  object,

  K,

  outminc = 5,

  outlg = 2,

  probthr = 0.001,

  thr = 2^-(1:40),

  outdistquant = 0.75,

  plot = TRUE,

  quiet = FALSE

)

}

\arguments{

\item{object}{\code{DISCBIO} class object.}

\item{K}{Number of clusters to be used.}

\item{outminc}{minimal transcript count of a gene in a clusters to be tested

for being an outlier gene. Default is 5.}

\item{outlg}{Minimum number of outlier genes required for being an outlier

cell. Default is 2.}

\item{probthr}{outlier probability threshold for a minimum of \code{outlg}

genes to be an outlier cell. This probability is computed from a negative

binomial background model of expression in a cluster. Default is 0.001.}

\item{thr}{probability values for which the number of outliers is computed in

order to plot the dependence of the number of outliers on the probability

threshold. Default is 2**-(1:40).set}

\item{outdistquant}{Real number between zero and one. Outlier cells are

merged to outlier clusters if their distance smaller than the

outdistquant-quantile of the distance distribution of  pairs of cells in

the orginal clusters after outlier removal. Default is 0.75.}

\item{plot}{if `TRUE`, produces a plot of -log10prob per K}

\item{quiet}{if `TRUE`, intermediary output is suppressed}

}

\value{

A named vector of the genes containing outlying cells and the number

  of cells on each.

}

\description{

This functions performs the outlier identification for k-means

and model-based clustering

}

\examples{

sc <- DISCBIO(valuesG1msTest)

sc <- Clustexp(sc, cln = 2) # K-means clustering

FindOutliers(sc, K = 2)

}