fix problem with scmapCell2Cluster

hemberg-lab · Dec 11, 2017 · fd54f6b · fd54f6b
1 parent a04281e
commit fd54f6b
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 15 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: scmap
 Type: Package
 Title: A tool for unsupervised projection of single cell RNA-seq data
-Version: 1.1.4
+Version: 1.1.5
 Author: Vladimir Kiselev
 Maintainer: Vladimir Kiselev <[email protected]>
 Authors@R: c(person("Vladimir", "Kiselev",

diff --git a/R/CoreMethods.R b/R/CoreMethods.R
@@ -475,4 +475,4 @@ scmapCell2Cluster.SingleCellExperiment <- function(scmapCell_results, cluster_li
 
 #' @rdname scmapCell2Cluster
 #' @aliases scmapCell2Cluster
-setMethod("scmapCell2Cluster", "SingleCellExperiment", scmapCell2Cluster.SingleCellExperiment)
+setMethod("scmapCell2Cluster", "list", scmapCell2Cluster.SingleCellExperiment)
diff --git a/man/scmapCell2Cluster.Rd b/man/scmapCell2Cluster.Rd
diff --git a/vignettes/scmap.Rmd b/vignettes/scmap.Rmd
@@ -206,13 +206,13 @@ names(scmapCell_results)
 For each dataset there are two matricies. `cells` matrix contains the top 10 (`scmap` default) cell IDs of the cells of the reference dataset that a given cell of the projection dataset is closest to:
 
 ```{r}
-scmapCell_results$xin$cells[,1:3]
+scmapCell_results$yan$cells[,1:3]
 ```
 
 `similarities` matrix contains corresponding cosine similarities:
 
 ```{r}
-scmapCell_results$xin$similarities[,1:3]
+scmapCell_results$yan$similarities[,1:3]
 ```
 
 ## Cluster annotation
@@ -221,7 +221,6 @@ If cell cluster annotation is available for the reference datasets, in addition
 
 ```{r}
 scmapCell_clusters <- scmapCell2Cluster(
-  sce, 
   scmapCell_results, 
   list(
     as.character(colData(sce)$cell_type1)