1. scone
  2. Commit 0d7200997b86c6960a3ea21e56de450214cf217f
Browse code

remove EDASeq and scran dependencies

Davide Risso authored on 30/06/2017 22:14:15
Showing 5 changed files
DESCRIPTION
History View file @ 0d72009
... ... 
@@ -25,8 +25,6 @@ Imports:
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   cluster,
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   compositions,
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   diptest,
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-  EDASeq,
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-  scran,
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   edgeR,
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   fpc,
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   gplots,
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@@ -50,6 +48,7 @@ Suggests:
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   plotly,
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   reshape2,
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   rmarkdown,
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+  scran,
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   scRNAseq,
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   shiny,
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   testthat,
NAMESPACE
History View file @ 0d72009
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@@ -81,7 +81,6 @@ importFrom(rhdf5,h5ls)
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 importFrom(rhdf5,h5read)
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 importFrom(rhdf5,h5write)
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 importFrom(rhdf5,h5write.default)
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-importFrom(scran,computeSumFactors)
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 importFrom(stats,approx)
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 importFrom(stats,as.formula)
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 importFrom(stats,binomial)
R/SCONE_DEFAULTS.R
History View file @ 0d72009
... ... 
@@ -3,11 +3,11 @@
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return Sum-scaled normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- SUM_FN(ei)
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-#'
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+#'
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 SUM_FN = function (ei) {
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   scales = colSums(ei)
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   eo = t(t(ei) * mean(scales) / scales)
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@@ -21,11 +21,11 @@ SUM_FN = function (ei) {
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return TMM normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- TMM_FN(ei)
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-#'
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+#'
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 TMM_FN = function(ei) {
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   size_fac = calcNormFactors(ei, method = "TMM")
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   scales = (colSums(ei) * size_fac)
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@@ -39,11 +39,11 @@ TMM_FN = function(ei) {
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return RLE normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- DESEQ_FN(ei)
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-#'
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+#'
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 DESEQ_FN = function(ei) {
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   size_fac = calcNormFactors(ei, method = "RLE")
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   scales = (colSums(ei) * size_fac)
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@@ -57,11 +57,11 @@ DESEQ_FN = function(ei) {
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return UQ normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- UQ_FN(ei)
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-#'
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+#'
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 UQ_FN = function(ei) {
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   size_fac = calcNormFactors(ei, method = "upperquartile")
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   scales = (colSums(ei) * size_fac)
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@@ -71,30 +71,30 @@ UQ_FN = function(ei) {
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 #' Full-quantile normalization wrapper function
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 #' @importFrom aroma.light normalizeQuantileRank.matrix
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-#' @details SCONE "scaling" wrapper for
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+#' @details SCONE "scaling" wrapper for
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 #'   \code{\link[aroma.light]{normalizeQuantileRank.matrix}}).
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return Full-quantile normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- FQ_FN(ei)
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-#'
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+#'
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 FQ_FN = function(ei) {
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   eo = normalizeQuantileRank.matrix(ei)
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   return(eo)
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 }
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 #' @rdname FQ_FN
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-#' @details Unlike FQ_FN, FQT_FN handles ties carefully (see
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+#' @details Unlike FQ_FN, FQT_FN handles ties carefully (see
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 #'   \code{\link[limma]{normalizeQuantiles}} for details).
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 #' @export
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- FQT_FN(ei)
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-#'
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+#'
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 FQT_FN = function(ei) {
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   eo = normalizeQuantileRank.matrix(ei, ties = TRUE)
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   return(eo)
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@@ -103,16 +103,16 @@ FQT_FN = function(ei) {
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 #' Centered log-ratio (CLR) normalization wrapper function
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 #' @importFrom compositions clr
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 #' @importFrom matrixStats colMedians
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-#' @details SCONE scaling wrapper for
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+#' @details SCONE scaling wrapper for
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 #'   \code{\link[compositions]{clr}}).
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return CLR normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:20,nrow = 7)
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 #' eo <- CLR_FN(ei)
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-#'
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+#'
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 CLR_FN = function (ei)
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 {
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   scale_mat <- t(clr(t(ei))) - log(ei)
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@@ -123,18 +123,21 @@ CLR_FN = function (ei)
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 }
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 #' Simple deconvolution normalization wrapper
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-#' @importFrom scran computeSumFactors
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 #' @details SCONE scaling wrapper for \code{\link[scran]{computeSumFactors}}).
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 #' @export
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 #' @param ei Numerical matrix. (rows = genes, cols = samples).
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 #' @return scran normalized matrix.
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-#'
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+#'
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 #' @examples
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 #' ei <- matrix(0:76,nrow = 7)
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 #' eo <- SCRAN_FN(ei)
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-#'
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+#'
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 SCRAN_FN = function(ei){
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-  scales = computeSumFactors(ei, sizes = ceiling(sqrt(ncol(ei))))
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+  if (!requireNamespace("scran", quietly = TRUE)) {
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+    stop("scran package needed for SCRAN_FN()")
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+  }
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+
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+  scales = scran::computeSumFactors(ei, sizes = ceiling(sqrt(ncol(ei))))
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   eo = t(t(ei) * mean(scales) / scales)
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   return(eo)
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-}
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\ No newline at end of file
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+}
man/CLR_FN.Rd
History View file @ 0d72009
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@@ -16,7 +16,7 @@ CLR normalized matrix.
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 Centered log-ratio (CLR) normalization wrapper function
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 }
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 \details{
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-SCONE scaling wrapper for
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+SCONE scaling wrapper for
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   \code{\link[compositions]{clr}}).
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 }
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 \examples{
man/FQ_FN.Rd
History View file @ 0d72009
... ... 
@@ -19,10 +19,10 @@ Full-quantile normalized matrix.
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 Full-quantile normalization wrapper function
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 }
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 \details{
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-SCONE "scaling" wrapper for
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+SCONE "scaling" wrapper for
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   \code{\link[aroma.light]{normalizeQuantileRank.matrix}}).
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-Unlike FQ_FN, FQT_FN handles ties carefully (see
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+Unlike FQ_FN, FQT_FN handles ties carefully (see
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   \code{\link[limma]{normalizeQuantiles}} for details).
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 }
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 \examples{