% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/get_normalized.R
\title{Retrieve Normalized Matrix}
get_normalized(x, method, ...)

\S4method{get_normalized}{SconeExperiment,character}(x, method, log = FALSE)

\S4method{get_normalized}{SconeExperiment,numeric}(x, method, log = FALSE)
\item{x}{a \code{\link{SconeExperiment}} object containing the results of 

\item{method}{character or numeric. Either a string identifying the 
normalization scheme to be retrieved, or a numeric index with the rank of 
the normalization method to retrieve (according to scone ranking of 

\item{...}{additional arguments for specific methods.}

\item{log}{logical. Should the data be returned in log-scale}
A matrix of normalized counts in log-scale.
Given a \code{SconeExperiment} object created by a call to scone, it will 
return a matrix of normalized counts (in log scale if \code{log=TRUE}).
If \code{\link{scone}} was run with \code{return_norm="in_memory"},
  this function simply retrieves the normalized data from the \code{assays} 
  slote of \code{object}.

If \code{\link{scone}} was run with \code{return_norm="hdf5"}, this
  function will read the normalized matrix from the specified hdf5 file.

If \code{\link{scone}} was run with \code{return_norm="no"}, this 
  function will compute the normalized matrix on the fly.

The numeric method will always return the normalization 
  corresponding to row \code{method} of the \code{scone_params} slot. This
  means that if \code{\link{scone}} was run with \code{eval=TRUE}, 
  \code{get_normalized(x, 1)} will return the top ranked method. If 
  \code{\link{scone}} was run with \code{eval=FALSE}, 
  \code{get_normalized(x,1)} will return the first normalization
  in the order saved by scone.
\section{Methods (by class)}{
\item \code{x = SconeExperiment,method = character}: If 
\code{method} is a character, it will return the normalized
matrix corresponding to the normalization scheme specified
by the character string.The string must be one of the 
\code{row.names} of the slot \code{scone_params}.

\item \code{x = SconeExperiment,method = numeric}: If 
\code{method} is a numeric, it will return the normalized
matrix according to the scone ranking.

mat <- matrix(rpois(500, lambda = 5), ncol=10)
colnames(mat) <- paste("X", 1:ncol(mat), sep="")
obj <- SconeExperiment(mat)
res <- scone(obj, scaling=list(none=identity, uq=UQ_FN),
           evaluate=TRUE, k_ruv=0, k_qc=0, 
           eval_kclust=2, bpparam = BiocParallel::SerialParam())
top_norm = get_normalized(res,1)