@@ -26,6 +26,7 @@ Imports:

   compositions,

   diptest,

   EDASeq,

+  scran,

   edgeR,

   fpc,

   gplots,

@@ -4,6 +4,7 @@ export(CLR_FN)

 export(DESEQ_FN)

 export(FQT_FN)

 export(FQ_FN)

+export(SCRAN_FN)

 export(SUM_FN)

 export(SconeExperiment)

 export(TMM_FN)

@@ -103,6 +104,7 @@ importFrom(rhdf5,h5ls)

 importFrom(rhdf5,h5read)

 importFrom(rhdf5,h5write)

 importFrom(rhdf5,h5write.default)

+importFrom(scran,computeSumFactors)

 importFrom(shiny,br)

 importFrom(shiny,brushedPoints)

 importFrom(shiny,column)

@@ -120,4 +120,21 @@ CLR_FN = function (ei)

   scales = exp(-colMedians(scale_mat, na.rm = TRUE))

   eo = t(t(ei) * mean(scales) / scales)

   return(eo)

+}

+

+#' Simple deconvolution normalization wrapper

+#' @importFrom scran computeSumFactors

+#' @details SCONE scaling wrapper for \code{\link[scran]{computeSumFactors}}).

+#' @export

+#' @param ei Numerical matrix. (rows = genes, cols = samples).

+#' @return scran normalized matrix.

+#'   

+#' @examples

+#' ei <- matrix(0:76,nrow = 7)

+#' eo <- SCRAN_FN(ei)

+#' 

+SCRAN_FN = function(ei){

+  scales = computeSumFactors(ei, sizes = ceiling(sqrt(ncol(ei))))

+  eo = t(t(ei) * mean(scales) / scales)

+  return(eo)

 }

\ No newline at end of file

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/SCONE_DEFAULTS.R

+\name{SCRAN_FN}

+\alias{SCRAN_FN}

+\title{Simple deconvolution normalization wrapper}

+\usage{

+SCRAN_FN(ei)

+}

+\arguments{

+\item{ei}{Numerical matrix. (rows = genes, cols = samples).}

+}

+\value{

+scran normalized matrix.

+}

+\description{

+Simple deconvolution normalization wrapper

+}

+\details{

+SCONE scaling wrapper for \code{\link[scran]{computeSumFactors}}).

+}

+\examples{

+ei <- matrix(0:76,nrow = 7)

+eo <- SCRAN_FN(ei)

+

+}