--- a
+++ b/man/Normalizedata.Rd
@@ -0,0 +1,77 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DIscBIO-generic-Normalizedata.R
+\name{Normalizedata}
+\alias{Normalizedata}
+\alias{Normalizedata,DISCBIO-method}
+\title{Normalizing and filtering}
+\usage{
+Normalizedata(
+  object,
+  mintotal = 1000,
+  minexpr = 0,
+  minnumber = 0,
+  maxexpr = Inf,
+  downsample = FALSE,
+  dsn = 1,
+  rseed = NULL
+)
+
+\S4method{Normalizedata}{DISCBIO}(
+  object,
+  mintotal = 1000,
+  minexpr = 0,
+  minnumber = 0,
+  maxexpr = Inf,
+  downsample = FALSE,
+  dsn = 1,
+  rseed = NULL
+)
+}
+\arguments{
+\item{object}{\code{DISCBIO} class object.}
+
+\item{mintotal}{minimum total transcript number required. Cells with less
+than \code{mintotal} transcripts are filtered out. Default is 1000.}
+
+\item{minexpr}{minimum required transcript count of a gene in at least
+\code{minnumber} cells. All other genes are filtered out. Default is 0.}
+
+\item{minnumber}{minimum number of cells that are expressing each gene at
+minexpr transcripts. Default is 0.}
+
+\item{maxexpr}{maximum allowed transcript count of a gene in at least a
+single cell after normalization or downsampling. All other genes are
+filtered out. Default is Inf.}
+
+\item{downsample}{A logical vector. Default is FALSE. If downsample is set to
+TRUE, then transcript counts are downsampled to mintotal transcripts per
+cell, instead of the normalization. Downsampled versions of the transcript
+count data are averaged across dsn samples}
+
+\item{dsn}{A numeric value of the number of samples to be used to average the
+downsampled versions of the transcript count data. Default is 1 which means
+that sampling noise should be comparable across cells. For high numbers of
+dsn the data will become similar to the median normalization.}
+
+\item{rseed}{Random integer to enforce reproducible clustering.
+results}
+}
+\value{
+The DISCBIO-class object input with the ndata and fdata slots filled.
+}
+\description{
+This function allows filtering of genes and cells to be used in
+  the downstream analysis.
+}
+\examples{
+sc <- DISCBIO(valuesG1msTest) # changes signature of data
+
+# In this case this function is used to normalize the reads
+sc_normal <- Normalizedata(
+  sc,
+  mintotal = 1000, minexpr = 0, minnumber = 0, maxexpr = Inf,
+  downsample = FALSE, dsn = 1, rseed = 17000
+)
+summary(sc_normal@fdata)
+
+}