add_assay_classification.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_assay_classification.R
\name{add_assay_classification}
\alias{add_assay_classification}
\title{Add Assay Classification to SE}
\usage{
add_assay_classification(
  summarized_experiment,
  mclust_result,
  check_colnames = TRUE,
  subset = TRUE,
  index = NULL,
  name = "classification"
)
}
\arguments{
\item{summarized_experiment}{SummarizedExperiment object}

\item{mclust_result}{Output of \code{\link[mclust]{mclust}} as list (of mclust outputs i.e. list) or single mclust output.}

\item{check_colnames}{Logical - should the "." in colnames be changed to "-"? | Default == TRUE ; TCGA IDs have "-" in their names, but in data frames they are changed to "."}

\item{subset}{Logical - subset summarized_experiment by names in mclust_result | Default == TRUE}

\item{index}{Integer - index of new assay}

\item{name}{Character - name of new assay}
}
\value{
SummarizedExperiment with new assay
}
\description{
Short function to add a classification matrix from mclust as an assay to a SummarizedExperiment object.
}
\details{
If length(mclust_result) is longer than nrow(summarized_experiment), this function will throw an error. Therefore you need to subset the SE first (subset = TRUE)
}