@@ -7,8 +7,8 @@

 runNormalization(

   inSCE,

   useAssay = "counts",

-  outAssayName = "customNormalizedAssay",

-  normalizationMethod = NULL,

+  outAssayName = "logcounts",

+  normalizationMethod = "logNormCounts",

   scale = FALSE,

   seuratScaleFactor = 10000,

   transformation = NULL,

@@ -2,12 +2,7 @@

 % Please edit documentation in R/runNormalization.R

 \name{runNormalization}

 \alias{runNormalization}

-\title{Wrapper function to run any of the integrated normalization/transformation

-methods in the singleCellTK. The available methods include 'LogNormalize',

-'CLR', 'RC' and 'SCTransform' from Seurat, 'logNormCounts and 'CPM' from

-Scater. Additionally, users can 'scale' using Z.Score, 'transform' using

-log, log1p and sqrt, add 'pseudocounts' and trim the final matrices

-between a range of values.}

+\title{Run normalization/transformation with various methods}

 \usage{

 runNormalization(

   inSCE,

@@ -47,11 +47,11 @@ selected assay. Options include `log2` (base 2 log transformation),

 `log1p` (natural log + 1 transformation) and `sqrt` (square root). Default

 value is \code{NULL}, which will not run any transformation.}

-\item{pseudocountsBeforeNorm}{Specify a numeric pseudo value that should be added 

+\item{pseudocountsBeforeNorm}{Specify a numeric pseudo value that should be added

 to the assay before normalization is performed. Default is \code{NULL},

 which will not add any value.}

-\item{pseudocountsBeforeTransform}{Specify a numeric pseudo value that should be 

+\item{pseudocountsBeforeTransform}{Specify a numeric pseudo value that should be

 added to the assay before transformation is run. Default is \code{NULL},

 which will not add any value.}

@@ -77,8 +77,8 @@ between a range of values.

 \examples{

 data(sce_chcl, package = "scds")

 sce_chcl <- runNormalization(

- inSCE = sce_chcl, 

- normalizationMethod = "SCTransform", 

- useAssay = "counts", 

- outAssayName = "sctCounts")

+ inSCE = sce_chcl,

+ normalizationMethod = "LogNormalize",

+ useAssay = "counts",

+ outAssayName = "logcounts")

 }

@@ -15,7 +15,7 @@ runNormalization(

   outAssayName = "customNormalizedAssay",

   normalizationMethod = NULL,

   scale = FALSE,

-  seuratScaleFactor = 10,

+  seuratScaleFactor = 10000,

   transformation = NULL,

   pseudocountsBeforeNorm = NULL,

   pseudocountsBeforeTransform = NULL,

@@ -39,7 +39,7 @@ normalization method.}

 Z.Score. Default \code{FALSE}.}

 \item{seuratScaleFactor}{Specify the `scaleFactor` argument if a Seurat

-normalization method is selected. Default is \code{10}. This parameter

+normalization method is selected. Default is \code{10000}. This parameter

 will not be used if methods other than seurat are selected.}

 \item{transformation}{Specify the transformation options to run on the

@@ -11,9 +11,9 @@ between a range of values.}

 \usage{

 runNormalization(

   inSCE,

-  normalizationMethod = NULL,

   useAssay = "counts",

-  normAssayName = "customNormalizedAssay",

+  outAssayName = "customNormalizedAssay",

+  normalizationMethod = NULL,

   scale = FALSE,

   seuratScaleFactor = 10,

   transformation = NULL,

@@ -26,15 +26,15 @@ runNormalization(

 \arguments{

 \item{inSCE}{Input \code{SingleCellExperiment} object.}

+\item{useAssay}{Specify the name of the assay that should be used.}

+

+\item{outAssayName}{Specify the name of the new output assay.}

+

 \item{normalizationMethod}{Specify a normalization method from `LogNormalize`,

 `CLR`, `RC` and `SCTransform` from Seurat or `logNormCounts` and `CPM` from

 scater packages. Default \code{NULL} is set which will not run any

 normalization method.}

-\item{useAssay}{Specify the name of the assay that should be used.}

-

-\item{normAssayName}{Specify the name of the new output assay.}

-

 \item{scale}{Logical value indicating if the data should be scaled using

 Z.Score. Default \code{FALSE}.}

@@ -78,7 +78,7 @@ between a range of values.

 data(sce_chcl, package = "scds")

 sce_chcl <- runNormalization(

  inSCE = sce_chcl, 

- "SCTransform", 

- "counts", 

- "sctCounts")

+ normalizationMethod = "SCTransform", 

+ useAssay = "counts", 

+ outAssayName = "sctCounts")

 }

@@ -19,8 +19,8 @@ runNormalization(

   transformation = NULL,

   pseudocountsBeforeNorm = NULL,

   pseudocountsBeforeTransform = NULL,

-  pseudocountsAfterTransform = NULL,

-  trim = NULL

+  trim = NULL,

+  verbose = TRUE

 )

 }

 \arguments{

@@ -55,14 +55,13 @@ which will not add any value.}

 added to the assay before transformation is run. Default is \code{NULL},

 which will not add any value.}

-\item{pseudocountsAfterTransform}{Specify a numeric pseudo value that should be 

-added to the assay after transformation is run. Default is \code{NULL},

-which will not add any value.}

-

 \item{trim}{Specify a vector of two numeric values that should be used

 as the upper and lower trim values to trim the assay between these two

 values. For example, \code{c(10,-10)} will trim the values between 10

 and -10. Default is \code{NULL}, which will not trim the data assay.}

+

+\item{verbose}{Logical value indicating if progress messages should be

+displayed to the user. Default is \code{TRUE}.}

 }

 \value{

 Output SCE object with new normalized/transformed assay stored.

@@ -17,8 +17,9 @@ runNormalization(

   scale = FALSE,

   seuratScaleFactor = 10,

   transformation = NULL,

-  pseudocountsNorm = NULL,

-  pseudocountsTransform = NULL,

+  pseudocountsBeforeNorm = NULL,

+  pseudocountsBeforeTransform = NULL,

+  pseudocountsAfterTransform = NULL,

   trim = NULL

 )

 }

@@ -46,18 +47,22 @@ selected assay. Options include `log2` (base 2 log transformation),

 `log1p` (natural log + 1 transformation) and `sqrt` (square root). Default

 value is \code{NULL}, which will not run any transformation.}

-\item{trim}{Specify a vector of two numeric values that should be used

-as the upper and lower trim values to trim the assay between these two

-values. For example, \code{c(10,-10)} will trim the values between 10

-and -10. Default is \code{NULL}, which will not trim the data assay.}

-

-\item{pseduoCountsNorm}{Specify a numeric pseudo value that should be added 

+\item{pseudocountsBeforeNorm}{Specify a numeric pseudo value that should be added 

 to the assay before normalization is performed. Default is \code{NULL},

 which will not add any value.}

-\item{pseduoCountsTransform}{Specify a numeric pseudo value that should be 

+\item{pseudocountsBeforeTransform}{Specify a numeric pseudo value that should be 

 added to the assay before transformation is run. Default is \code{NULL},

 which will not add any value.}

+

+\item{pseudocountsAfterTransform}{Specify a numeric pseudo value that should be 

+added to the assay after transformation is run. Default is \code{NULL},

+which will not add any value.}

+

+\item{trim}{Specify a vector of two numeric values that should be used

+as the upper and lower trim values to trim the assay between these two

+values. For example, \code{c(10,-10)} will trim the values between 10

+and -10. Default is \code{NULL}, which will not trim the data assay.}

 }

 \value{

 Output SCE object with new normalized/transformed assay stored.

@@ -3,7 +3,11 @@

 \name{runNormalization}

 \alias{runNormalization}

 \title{Wrapper function to run any of the integrated normalization/transformation

-methods in the singleCellTK.}

+methods in the singleCellTK. The available methods include 'LogNormalize',

+'CLR', 'RC' and 'SCTransform' from Seurat, 'logNormCounts and 'CPM' from

+Scater. Additionally, users can 'scale' using Z.Score, 'transform' using

+log, log1p and sqrt, add 'pseudocounts' and trim the final matrices

+between a range of values.}

 \usage{

 runNormalization(

   inSCE,

@@ -19,24 +23,52 @@ runNormalization(

 )

 }

 \arguments{

-\item{inSCE}{input}

+\item{inSCE}{Input \code{SingleCellExperiment} object.}

-\item{normalizationMethod}{normal}

+\item{normalizationMethod}{Specify a normalization method from `LogNormalize`,

+`CLR`, `RC` and `SCTransform` from Seurat or `logNormCounts` and `CPM` from

+scater packages. Default \code{NULL} is set which will not run any

+normalization method.}

-\item{useAssay}{use}

+\item{useAssay}{Specify the name of the assay that should be used.}

-\item{normAssayName}{npr}

+\item{normAssayName}{Specify the name of the new output assay.}

-\item{scale}{scale}

+\item{scale}{Logical value indicating if the data should be scaled using

+Z.Score. Default \code{FALSE}.}

-\item{seuratScaleFactor}{factor}

+\item{seuratScaleFactor}{Specify the `scaleFactor` argument if a Seurat

+normalization method is selected. Default is \code{10}. This parameter

+will not be used if methods other than seurat are selected.}

+

+\item{transformation}{Specify the transformation options to run on the

+selected assay. Options include `log2` (base 2 log transformation),

+`log1p` (natural log + 1 transformation) and `sqrt` (square root). Default

+value is \code{NULL}, which will not run any transformation.}

+

+\item{trim}{Specify a vector of two numeric values that should be used

+as the upper and lower trim values to trim the assay between these two

+values. For example, \code{c(10,-10)} will trim the values between 10

+and -10. Default is \code{NULL}, which will not trim the data assay.}

+

+\item{pseduoCountsNorm}{Specify a numeric pseudo value that should be added 

+to the assay before normalization is performed. Default is \code{NULL},

+which will not add any value.}

+

+\item{pseduoCountsTransform}{Specify a numeric pseudo value that should be 

+added to the assay before transformation is run. Default is \code{NULL},

+which will not add any value.}

 }

 \value{

-object

+Output SCE object with new normalized/transformed assay stored.

 }

 \description{

 Wrapper function to run any of the integrated normalization/transformation

-methods in the singleCellTK.

+methods in the singleCellTK. The available methods include 'LogNormalize',

+'CLR', 'RC' and 'SCTransform' from Seurat, 'logNormCounts and 'CPM' from

+Scater. Additionally, users can 'scale' using Z.Score, 'transform' using

+log, log1p and sqrt, add 'pseudocounts' and trim the final matrices

+between a range of values.

 }

 \examples{

 data(sce_chcl, package = "scds")

@@ -2,15 +2,20 @@

 % Please edit documentation in R/runNormalization.R

 \name{runNormalization}

 \alias{runNormalization}

-\title{Title}

+\title{Wrapper function to run any of the integrated normalization/transformation

+methods in the singleCellTK.}

 \usage{

 runNormalization(

   inSCE,

-  normalizationMethod,

-  useAssay,

-  normAssayName,

+  normalizationMethod = NULL,

+  useAssay = "counts",

+  normAssayName = "customNormalizedAssay",

   scale = FALSE,

-  seuratScaleFactor

+  seuratScaleFactor = 10,

+  transformation = NULL,

+  pseudocountsNorm = NULL,

+  pseudocountsTransform = NULL,

+  trim = NULL

 )

 }

 \arguments{

@@ -30,7 +35,8 @@ runNormalization(

 object

 }

 \description{

-Title

+Wrapper function to run any of the integrated normalization/transformation

+methods in the singleCellTK.

 }

 \examples{

 data(sce_chcl, package = "scds")

new file mode 100644

@@ -0,0 +1,42 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runNormalization.R

+\name{runNormalization}

+\alias{runNormalization}

+\title{Title}

+\usage{

+runNormalization(

+  inSCE,

+  normalizationMethod,

+  useAssay,

+  normAssayName,

+  scale = FALSE,

+  seuratScaleFactor

+)

+}

+\arguments{

+\item{inSCE}{input}

+

+\item{normalizationMethod}{normal}

+

+\item{useAssay}{use}

+

+\item{normAssayName}{npr}

+

+\item{scale}{scale}

+

+\item{seuratScaleFactor}{factor}

+}

+\value{

+object

+}

+\description{

+Title

+}

+\examples{

+data(sce_chcl, package = "scds")

+sce_chcl <- runNormalization(

+ inSCE = sce_chcl, 

+ "SCTransform", 

+ "counts", 

+ "sctCounts")

+}