Fix for issue 2

cole-trapnell-lab · Feb 8, 2019 · 2955829 · 2955829
1 parent 97c5125
commit 2955829
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Showing 7 changed files with 25 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: garnett
 Type: Package
 Title: Automated cell type classification
-Version: 0.1.0
+Version: 0.1.1
 Author: c(
     person("Hannah", "Pliner", email = "[email protected]", role = c("aut", "cre")), 
     person("Cole", "Trapnell", email = "[email protected]", role = c("aut")))

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
+export(check_markers)
+export(classify_cells)
+export(get_classifier_references)
+export(get_feature_genes)
+export(plot_markers)
+export(train_cell_classifier)
+exportClasses(cell_rules)
+exportClasses(garnett_classifier)
+exportClasses(gene_rule)
 import(monocle)
 importFrom(Biobase,"fData<-")
 importFrom(Biobase,"pData<-")

diff --git a/R/train_cell_classifier.R b/R/train_cell_classifier.R
@@ -387,6 +387,8 @@ make_name_map <- function(parse_list,
     gene_table <- merge(gene_table, possibles, all.x=T,
                         by.x="fgenes", by.y="ensembl")
     gene_table$fgenes <- gene_table$cds
+  } else {
+    gene_table$cds <- gene_table$fgenes
   }
 
   gene_table$in_cds <- gene_table$f %in% possible_genes

diff --git a/man/check_markers.Rd b/man/check_markers.Rd
diff --git a/man/garnett_classifier.Rd b/man/garnett_classifier.Rd
diff --git a/man/get_feature_genes.Rd b/man/get_feature_genes.Rd
diff --git a/man/train_cell_classifier.Rd b/man/train_cell_classifier.Rd