Export functions to get expression matrix and default embedding. Add …

…man/*.Rd files.
aertslab · Nov 8, 2018 · 34956c5 · 34956c5
1 parent 97fa404
commit 34956c5
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Showing 14 changed files with 76 additions and 442 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,6 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+.RData
+.Ruserdata
+.gitignore
+tests/*
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,4 +11,4 @@ Suggests: seurat, stringr
 License: Apache-2
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -21,11 +21,14 @@ export(finalize)
 export(flush)
 export(get_cell_ids)
 export(get_col_attr_by_key)
+export(get_default_embedding)
+export(get_dgem)
 export(get_dtype)
 export(get_genes)
 export(get_global_attr)
 export(get_global_meta_data)
 export(get_seurat_clustering_resolutions)
+export(hierarchy_exists)
 export(init_global_md_embeddings)
 export(lookup_all_global_attr)
 export(lookup_loom)

diff --git a/R/loom.R b/R/loom.R
@@ -1417,6 +1417,7 @@ get_genes<-function(loom
 #'@description Get the expression matrix for the given .loom.
 #'@param loom The loom file handler.
 #'@return The gene expression matrix (genes as rows, cells as columns).
+#'@export
 get_dgem<-function(loom) {
   dgem<-t(loom[["matrix"]][,])
   cell.ids<-get_cell_ids(loom = loom)
@@ -1431,6 +1432,7 @@ get_dgem<-function(loom) {
 #'@description Get the default embedding for the given .loom.
 #'@param loom The loom file handler.
 #'@return The default embedding.
+#'@export
 get_default_embedding<-function(loom) {
   return (loom[["col_attrs"]][[CA_EMBEDDING_NAME]])
 }

diff --git a/inst/doc/SCopeLoomR_tutorial.html b/inst/doc/SCopeLoomR_tutorial.html
diff --git a/man/add_global_md_clustering.Rd b/man/add_global_md_clustering.Rd
diff --git a/man/add_global_md_embedding.Rd b/man/add_global_md_embedding.Rd
diff --git a/man/add_hierarchy.Rd b/man/add_hierarchy.Rd
diff --git a/man/add_scenic_regulons.Rd b/man/add_scenic_regulons.Rd
diff --git a/man/add_seurat_clustering.Rd b/man/add_seurat_clustering.Rd
diff --git a/man/build_loom.Rd b/man/build_loom.Rd
diff --git a/man/check_missings.Rd b/man/check_missings.Rd
diff --git a/man/hierarchy_exists.Rd b/man/hierarchy_exists.Rd
diff --git a/man/is_order_conserved.Rd b/man/is_order_conserved.Rd