--- a
+++ b/man/normalizeData.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/allgenerics.R, R/processing.R
+\name{normalizeData}
+\alias{normalizeData}
+\alias{normalizeData,VoltRon-method}
+\alias{normalizeData,vrAssay-method}
+\alias{normalizeData,vrAssayV2-method}
+\title{Normalize Data}
+\usage{
+normalizeData(object, ...)
+
+\S4method{normalizeData}{VoltRon}(
+  object,
+  assay = NULL,
+  method = "LogNorm",
+  desiredQuantile = 0.9,
+  scale = 0.2,
+  sizefactor = 10000,
+  feat_type = NULL
+)
+
+\S4method{normalizeData}{vrAssay}(
+  object,
+  method = "LogNorm",
+  desiredQuantile = 0.9,
+  scale = 0.2,
+  sizefactor = 10000,
+  feat_type = NULL
+)
+
+\S4method{normalizeData}{vrAssayV2}(
+  object,
+  method = "LogNorm",
+  desiredQuantile = 0.9,
+  scale = 0.2,
+  sizefactor = 10000,
+  feat_type = NULL
+)
+}
+\arguments{
+\item{object}{a VoltRon or vrAssay object.}
+
+\item{...}{arguments passed to other methods.}
+
+\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 
+if NULL, the default assay will be used, see \link{vrMainAssay}.}
+
+\item{method}{the normalization method: "LogNorm", "Q3Norm", "LogQ3Norm" or "CLR"}
+
+\item{desiredQuantile}{the quantile of the data if "QuanNorm" or "LogQuanNorm" is selected as \code{method}.}
+
+\item{scale}{the scale parameter for the hyperbolic arcsine transformation}
+
+\item{sizefactor}{size factor if \code{method} is selected as \code{LogNorm}}
+
+\item{feat_type}{the feature set type}
+}
+\description{
+Given a VoltRon or vrAssay object, normalize the raw count data.
+}