fix idf calc bug

cole-trapnell-lab · Oct 16, 2019 · 0c1efdb · 0c1efdb
1 parent e278c65
commit 0c1efdb
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: garnett
 Type: Package
 Title: Automated cell type classification
-Version: 0.2.7
+Version: 0.2.8
 Author: c(
     person("Hannah", "Pliner", email = "[email protected]", role = c("aut", "cre")), 
     person("Cole", "Trapnell", email = "[email protected]", role = c("aut")))

diff --git a/R/train_cell_classifier.R b/R/train_cell_classifier.R
@@ -592,7 +592,7 @@ tfidf <- function(input_cds) {
   ncounts <- ncounts[Matrix::rowSums(ncounts) != 0,]
   nfreqs <- ncounts
   nfreqs@x <- ncounts@x / rep.int(Matrix::colSums(ncounts), diff(ncounts@p))
-  tf_idf_counts <- nfreqs * log(1 + ncol(ncounts) / Matrix::rowSums(ncounts))
+  tf_idf_counts <- nfreqs * log(1 + ncol(ncounts) / Matrix::rowSums(ncounts > 0))
   Matrix::t(tf_idf_counts)
 }