processOneCancerGroup.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/TCGAFunctions.R
\name{processOneCancerGroup}
\alias{processOneCancerGroup}
\title{processOneCancerGroup
Processes one cancer group}
\usage{
processOneCancerGroup(cancerData, minExpressedPercentage = 2,
  algorithm = "mclust", maxModality = 3, minClusterSize = 50,
  minSamples = NULL, pathToClinicalData = "pathToClinicalData",
  pathToExpressionmatrix = "pathToExpressionmatrix", SilvermanP = 0.05,
  verbose = TRUE)
}
\arguments{
\item{cancerData}{TCGA cancer expression data of one cancer group}

\item{minExpressedPercentage}{integer specifying the percentage of patients that should at least be expressed for the gene to be analysed}

\item{algorithm}{"mclust", "hdbscan" or "flexmix". Defines which algorithm should be used to process the cancer data}

\item{maxModality}{An integer specifying the highest modality to calculate models in with mclust and flexmix}

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

\item{minSamples}{Integer for hdbscan; 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{pathToClinicalData}{path to the clinical data}

\item{pathToExpressionmatrix}{path to the expression matrix}

\item{SilvermanP}{The p-value that is used to reject Silvermans Test for unimodality
(given by k=1 using the Hall/York adjustments)}

\item{verbose}{logical. Whether to print progress messages}
}
\description{
processOneCancerGroup
Processes one cancer group
}
\details{
Processes one cancer group by a) filtering 0 sum rows,
b) using Silverman's test for unimodality,
c) filtering genes with <2% of patients that have expression values greater 0,
d) use useMclust on cancer data,
e) creating list of output and filtered expression matrix
}