add_assay_norm.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_assay_norm.R
\name{add_assay_norm}
\alias{add_assay_norm}
\title{Add Assay of Normalized Counts}
\usage{
add_assay_norm(
  summarized_experiment,
  assay_index = 1,
  method = "TMM",
  calc_operation = "division",
  new_index = NULL,
  name = "normalizedCounts",
  add_info_metadata = T
)
}
\arguments{
\item{summarized_experiment}{SummarizedExperiment}

\item{assay_index}{Integer - index of assay or a matrix or dataframe the normalization factor is to be calculated from.}

\item{method}{Character - method for calculation used by \code{\link[edgeR]{calcNormFactors}}}

\item{calc_operation}{Character - how the values are normalized | Either by "division" or "multiplication"}

\item{new_index}{Integer - the index new assay is stored in | Should not be 1}

\item{name}{Character - name of new assay}

\item{add_info_metadata}{Logical - save information of changes in meta data?}
}
\value{
SummarizedExperiment with new assay of normalized counts.
}
\description{
This function adds a new assay with normalized counts to the SE. Normalization is done with any Method of edgeR. Standard method is TMM
}
\details{
The rows are either multiplicated or devided by the normalization factor.
}
\examples{

}