Move sctransform from suggests to imports

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 3.0.0.9150
+Version: 3.0.0.9200
 Date: 2019-04-16
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
@@ -51,6 +51,7 @@ Imports:
     rsvd,
     Rtsne,
     scales,
+    sctransform (>= 0.2.0),
     SDMTools,
     stats,
     tools,
@@ -77,7 +78,6 @@ RoxygenNote: 6.1.1
 Encoding: UTF-8
 Suggests:
     testthat,
-    sctransform,
     hdf5r,
     S4Vectors,
     SummarizedExperiment,

NAMESPACE

@@ -459,6 +459,10 @@ importFrom(rlang,"!!")
 importFrom(rsvd,rsvd)
 importFrom(scales,hue_pal)
 importFrom(scales,zero_range)
+importFrom(sctransform,correct_counts)
+importFrom(sctransform,get_residual_var)
+importFrom(sctransform,get_residuals)
+importFrom(sctransform,vst)
 importFrom(stats,aggregate)
 importFrom(stats,anova)
 importFrom(stats,approxfun)

R/preprocessing.R

@@ -1007,6 +1007,7 @@ SampleUMI <- function(
 #' @param ... Additional parameters passed to \code{sctransform::vst}
 #'
 #' @importFrom stats setNames
+#' @importFrom sctransform vst get_residual_var get_residuals correct_counts
 #'
 #' @export
 #'
@@ -1081,8 +1082,8 @@ SCTransform <- function(
   }
   if (conserve.memory) {
     vst.args[['residual_type']] <- 'none'
-    vst.out <- do.call(what = sctransform::vst, args = vst.args)
-    feature.variance <- sctransform::get_residual_var(
+    vst.out <- do.call(what = 'vst', args = vst.args)
+    feature.variance <- get_residual_var(
       vst_out = vst.out,
       umi = umi,
       residual_type = residual.type,
@@ -1091,7 +1092,7 @@ SCTransform <- function(
     vst.out$gene_attr$residual_variance <- NA_real_
     vst.out$gene_attr[names(x = feature.variance), 'residual_variance'] <- feature.variance
   } else {
-    vst.out <- do.call(what = sctransform::vst, args = vst.args)
+    vst.out <- do.call(what = 'vst', args = vst.args)
     feature.variance <- setNames(
       object = vst.out$gene_attr$residual_variance,
       nm = rownames(x = vst.out$gene_attr)
@@ -1114,14 +1115,14 @@ SCTransform <- function(
     if (verbose) {
       message("Return only variable features for scale.data slot of the output assay")
     }
-    vst.out$y <- sctransform::get_residuals(
+    vst.out$y <- get_residuals(
       vst_out = vst.out,
       umi = umi[top.features, ],
       residual_type = residual.type,
       res_clip_range = res.clip.range
     )
     if (do.correct.umi & residual.type == 'pearson') {
-      vst.out$umi_corrected <- sctransform::correct_counts(
+      vst.out$umi_corrected <- correct_counts(
         x = vst.out,
         umi = umi,
         show_progress = verbose

README.md

@@ -3,7 +3,7 @@
 [![CRAN Version](https://www.r-pkg.org/badges/version/Seurat)](https://cran.r-project.org/package=Seurat)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Seurat)](https://cran.r-project.org/package=Seurat)
 
-# Seurat v3.0.0.9150 - Beta
+# Seurat v3.0.0.9200 - Beta
 
 Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.