Add examples for as.Seurat and as.loom

satijalab · Mar 29, 2019 · 6d361c0 · 6d361c0
1 parent 08dc0eb
commit 6d361c0
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Showing 4 changed files with 29 additions and 1 deletion.
diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R
@@ -1099,7 +1099,7 @@ RunTSNE.Seurat <- function(
       add.iter = add.iter,
       dim.embed = dim.embed,
       reduction.key = reduction.key,
-      is_distance = TRUE, 
+      is_distance = TRUE,
       ...
     )
   } else if (!is.null(x = dims)) {
@@ -1501,6 +1501,10 @@ ScoreJackStraw.Seurat <- function(
   return(object)
 }
 
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+# Methods for R-defined generics
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # Internal
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

diff --git a/R/objects.R b/R/objects.R
@@ -1235,6 +1235,11 @@ as.Graph.matrix <- function(x, ...) {
 #' @export
 #' @method as.loom Seurat
 #'
+#' @examples
+#' \dontrun{
+#' lfile <- as.loom(x = pbmc_small)
+#' }
+#'
 as.loom.Seurat <- function(
   x,
   assay = NULL,
@@ -1406,6 +1411,12 @@ as.loom.Seurat <- function(
 #' @export
 #' @method as.Seurat loom
 #'
+#' @examples
+#' \dontrun{
+#' lfile <- as.loom(x = pbmc_small)
+#' pbmc <- as.Seurat(x = lfile)
+#' }
+#'
 as.Seurat.loom <- function(
   x,
   cells = 'CellID',

diff --git a/man/as.Seurat.Rd b/man/as.Seurat.Rd
diff --git a/man/as.loom.Rd b/man/as.loom.Rd