normaliseDGE.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/normalise.R
\name{normaliseDGE}
\alias{normaliseDGE}
\title{Normalise Digital Gene Expression Matrix}
\usage{
normaliseDGE(dge, verbose = FALSE, center = TRUE, scale = TRUE,
  outliers = FALSE, threshold = 5, min_library_size = 200,
  gene_subset = 0.5, transformation = "sqrt")
}
\arguments{
\item{dge}{matrix; a digital gene expression matrix containing count data (columns = cells, rows = genes), can be a sparce Matrix object.}

\item{verbose}{logical; if TRUE the function will print diagnostic graphs along the way}

\item{center}{logical; if true genes are centered to mean of 0}

\item{scale}{logical; if TRUE genes are scaled to unit variance}

\item{outliers}{logical; calculate max value per gene and cell to assess threshold position}

\item{threshold}{integer; any normalised values larger than this will be rounded down}

\item{min_library_size}{real; only cells with library size equal or greater to this will be kept}

\item{gene_subset}{real; what fraction of the genes do you want to keep (by mean) e.g. 0.5 is top half most expressed}

\item{transformation}{character; either sqrt (default) or asinh}
}
\value{
A matrix of read counts
}
\description{
\code{normaliseDGE} normalise a gene by cell matrix
}
\examples{
# normalised_counts <- normalise_dge(dge)
}