% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/main.R
\name{computeMultivariateSupport}
\alias{computeMultivariateSupport}
\title{Estimate the baseline support}
\usage{
computeMultivariateSupport(seMat, FeatureSets, gamma = 0.1,
  beta = 0.95, distance = "euclidean", verbose = TRUE)
}
\arguments{
\item{seMat}{SummariziedExperiment with an assay in [0, 1], with each column corresponding to a sample and each 
row corresponding to a feature; usually in quantile form.}

\item{FeatureSets}{The multivariate features in list or matrix form. In list form, each list element
should be a vector of individual features; in matrix form, it should be a binary matrix with rownames
being individual features and column names being the names of the feature sets.}

\item{gamma}{Parameter for selecting radius around each support point (0 < gamma < 1).
By default gamma = 0.1.}

\item{beta}{Parameter for eliminating outliers (0 < beta <= 1). By default beta=0.95.}

\item{distance}{Type of distance to be calculated between points. Any type of distance that can be passed on
to the dist function can be used (default 'euclidean').}

\item{verbose}{Logical indicating whether to print status related messages during computation (defaults
to TRUE).}
}
\value{
A list with elements:
	Support: a matrix indicating which samples were included in the support.
	Baseline_list: a list where each element is the baseline of a multivariate feature. 
	featureMat: the multivariate features in matrix form.
	alpha: the expected number of divergent multivariate features per sample.
	gamma: the gamma parameter used for baseline computation.
	distance: the type of distance used for baselien computation.
}
\description{
Function for computing the basline support for multivariate features given gamma
and beta parameters.
}
\examples{
baseMat = breastTCGA_Mat[, breastTCGA_Group == "NORMAL"]
seMat.base = SummarizedExperiment(assays=list(data=baseMat))
assays(seMat.base)$quantile = computeQuantileMatrix(seMat.base)
baseline = computeMultivariateSupport(seMat=seMat.base, FeatureSets=msigdb_Hallmarks)

}
\keyword{baseline,}
\keyword{support}
