Change input data for trajectory analysis with Monocle as mentioned in …

…#21.
romanhaa · Jun 17, 2020 · feb6f53 · feb6f53
1 parent 34f98c7
commit feb6f53
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Showing 6 changed files with 24 additions and 24 deletions.
diff --git a/examples/GSE108041/Seurat_v3/README.md b/examples/GSE108041/Seurat_v3/README.md
@@ -277,8 +277,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -302,8 +302,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 

diff --git a/examples/GSE108041/scanpy/README.md b/examples/GSE108041/scanpy/README.md
@@ -353,8 +353,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -378,8 +378,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 

diff --git a/examples/GSE129845/Seurat_v3/README.md b/examples/GSE129845/Seurat_v3/README.md
@@ -341,8 +341,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -366,8 +366,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 

diff --git a/examples/pbmc_10k_v3/Seurat_v2/README.md b/examples/pbmc_10k_v3/Seurat_v2/README.md
@@ -286,8 +286,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@data),
-    row.names = rownames(seurat@data))
+    gene_short_name = rownames(seurat@counts),
+    row.names = rownames(seurat@counts))
   )
 )
 
@@ -311,8 +311,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@data),
-    row.names = rownames(seurat@data))
+    gene_short_name = rownames(seurat@counts),
+    row.names = rownames(seurat@counts))
   )
 )
 

diff --git a/examples/pbmc_10k_v3/Seurat_v3/README.md b/examples/pbmc_10k_v3/Seurat_v3/README.md
@@ -233,8 +233,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -258,8 +258,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 

diff --git a/examples/pbmc_10k_v3/scanpy/README.md b/examples/pbmc_10k_v3/scanpy/README.md
@@ -321,8 +321,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -346,8 +346,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )