Merge pull request #26 from CCBR/pkg-doc

docs: create package doc

Author: kelly-sovacool

NAMESPACE

@@ -0,0 +1,13 @@
+#' SCOT: Toolbox for single cell RNA-seq
+#'
+#' Designed for single-cell RNA-seq analysis with [SINCLAIR](https://github.com/CCBR/SINCLAIR).
+#'
+#' See the website for more information, documentation, and examples:
+#'   \url{https://ccbr.github.io/SCOT}
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/SCOT-package.R

@@ -53,7 +53,7 @@ filter_doublets <- function(so_in, doublet_finder_method = "DoubletFinder") {
     so_in <- subset(so_in, cells = colnames(so_in)[which(so_in$doubletFinder_label == "Singlet")])
   } else if (doublet_finder_method == "scDblFinder") {
     sce <- Seurat::as.SingleCellExperiment(so_in)
-    sce_dbl <- scDblFinder::scDblFinder(sce) %>% suppressWarnings()
+    sce_dbl <- scDblFinder::scDblFinder(sce) |> suppressWarnings()
     so_in$scDblFinder_label <- sce_dbl$scDblFinder.class
     so_in <- subset(so_in, cells = colnames(so_in)[which(so_in$scDblFinder_label == "singlet")])
   } else if (doublet_finder_method == "union") {
@@ -91,7 +91,7 @@ filter_doublets <- function(so_in, doublet_finder_method = "DoubletFinder") {
     so_in$doubletFinder_label <- dfso[[utils::tail(names(dfso@meta.data), 1)]]
 
     sce <- Seurat::as.SingleCellExperiment(so_in)
-    sce_dbl <- scDblFinder::scDblFinder(sce) %>% suppressWarnings()
+    sce_dbl <- scDblFinder::scDblFinder(sce) |> suppressWarnings()
     so_in$scDblFinder_label <- sce_dbl$scDblFinder.class
     so_in <- subset(so_in, cells = colnames(so_in)[intersect(
       which(so_in$doubletFinder_label == "Singlet"),
@@ -132,7 +132,7 @@ filter_doublets <- function(so_in, doublet_finder_method = "DoubletFinder") {
     so_in$doubletFinder_label <- dfso[[utils::tail(names(dfso@meta.data), 1)]]
 
     sce <- Seurat::as.SingleCellExperiment(so_in)
-    sce_dbl <- scDblFinder::scDblFinder(sce) %>% suppressWarnings()
+    sce_dbl <- scDblFinder::scDblFinder(sce) |> suppressWarnings()
     so_in$scDblFinder_label <- sce_dbl$scDblFinder.class
     so_in <- subset(so_in, cells = colnames(so_in)[unique(c(
       which(so_in$doubletFinder_label == "Singlet"),

R/filter_doublets.R

@@ -1,13 +1,3 @@
-#' dplyr pipe
-#' @importFrom dplyr %>%
-#' @export
-dplyr::`%>%`
-
-#' magrittr assignment pipe
-#' @importFrom magrittr %<>%
-#' @export
-magrittr::`%<>%`
-
 #' walrus operator
 #' @importFrom rlang :=
 #' @export
@@ -21,7 +11,7 @@ rlang::.data
 
 # Suppress R CMD check note 'All declared Imports should be used'.
 # These packages are used by Seurat, but are only listed in Seurat's Suggests field.
-# See \url{https://community.rstudio.com/t/how-should-a-meta-package-handle-this-note-all-declared-imports-should-be-used/23400/3}
+# https://community.rstudio.com/t/how-should-a-meta-package-handle-this-note-all-declared-imports-should-be-used/23400/3
 #' @importFrom harmony RunHarmony
 #' @importFrom rliger createLiger
 NULL