% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/fracfixr.r
\name{get_corrected_counts}
\alias{get_corrected_counts}
\title{get_corrected_counts: Retrieve the Corrected Count Matrix}
\usage{
get_corrected_counts(fracfixr_results)
}
\arguments{
\item{fracfixr_results}{Output list from \code{\link{FracFixR}}, which must
contain the element \code{NewData} (present in results from version >= 1.1.0).}
}
\value{
A numeric matrix with the same dimensions as
  \code{fracfixr_results$Propestimates}. Non-Total columns contain corrected
  counts (rounded integers, proportion estimate multiplied by the
  NNLS-predicted total abundance). The Total column contains the
  NNLS-predicted total abundance itself.
}
\description{
Returns the corrected count matrix embedded in a \code{FracFixR()} result
object. This matrix is computed internally by multiplying each transcript's
proportion estimate by the predicted total abundance for that replicate,
providing counts that are corrected for compositional bias while remaining
on the original count scale.

If you need to re-scale using the raw (observed) Total counts instead of the
NNLS-predicted totals, multiply \code{fracfixr_results$Propestimates} by the
corresponding column of \code{fracfixr_results$OriginalData} manually.
}
\examples{
data(example_counts)
data(example_annotation)

results <- FracFixR(example_counts, example_annotation, parallel = FALSE)
corrected <- get_corrected_counts(results)
head(corrected)

}
