useHdbscan.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/algorithmSpecificFunctions.R
\name{useHdbscan}
\alias{useHdbscan}
\title{UseHdbscan}
\usage{
useHdbscan(expression, minClusterSize = 10, minSamples = NULL,
  verbose = TRUE, pathToClinicalData = "pathTo/clinicalData",
  pathToExpressionmatrix = "pathTo/expressionmatrix")
}
\arguments{
\item{expression}{(Simulated) Gene Expression data frame which genes shall
be classified as unimodal, bimodal or other}

\item{minClusterSize}{** Integer; The minimum number of samples
in a group for that group to be considered a cluster}

\item{minSamples}{** Integer; The number of samples
in a neighborhood for a point to be considered as a core point.
This includes the point itself. If NULL: defaults to the min_cluster_size.}

\item{verbose}{logical. Whether to print progress messages}

\item{pathToClinicalData}{If real data is used the path
to the clinical data can be stored here}

\item{pathToExpressionmatrix}{If real data is used the path
to the gene expression matrix can be stored here}
}
\value{
hdbscanOutput The formatted output of the HDBSCAN clustering
}
\description{
Use the HDBSCAN algorithm for generating output to evaluate the
classification (unimodal,bimodal or other) of genes.
}
\details{
For details on how HDBSCAN works and
for details on what parameters with ** do,
see http://hdbscan.readthedocs.io/en/latest/
}
\examples{
\dontrun{
params <- newParams(nGenes = list("1"=10,"2"=list("gauss"= 10,"gamma"= 10)))
simulation <- simulateExpression(params= params,verbose=FALSE)
expression <- simulation$expressionData
#with messages printed to console
hdbscanOutput <- useHdbscan(expression = expression)
#with specified minPts parameter
hdbscanOutput <- useHdbscan(expression = expression, minClusterSize = 15)
#without messages printed to console
hdbscanOutput <- useHdbscan(expression = expression, verbose = FALSE)
}
}