Fix bug introduced in 0.1.2 plus suppress new cds warnings

cole-trapnell-lab · Feb 12, 2019 · d04a89b · d04a89b
1 parent f2e1024
commit d04a89b
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Showing 4 changed files with 15 additions and 17 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: garnett
 Type: Package
 Title: Automated cell type classification
-Version: 0.1.2
+Version: 0.1.3
 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/classify_cells.R b/R/classify_cells.R
@@ -98,9 +98,9 @@ classify_cells <- function(cds,
     sf <- pData(cds)$Size_Factor
     pd <- new("AnnotatedDataFrame", data = pData(cds))
     fd <- new("AnnotatedDataFrame", data = fData(cds))
-    cds <- newCellDataSet(as(exprs(cds), "dgCMatrix"),
+    cds <- suppressWarnings(newCellDataSet(as(exprs(cds), "dgCMatrix"),
                           phenoData = pd,
-                          featureData = fd)
+                          featureData = fd))
     pData(cds)$Size_Factor <- sf
   }
 
@@ -116,8 +116,8 @@ classify_cells <- function(cds,
   fd <- new("AnnotatedDataFrame", data = fData(cds))
   temp <- exprs(cds)
   temp@x <- temp@x / rep.int(pData(cds)$Size_Factor, diff(temp@p))
-  norm_cds <- newCellDataSet(temp,
-                             phenoData = pd, featureData = fd)
+  norm_cds <- suppressWarnings(newCellDataSet(temp,
+                             phenoData = pd, featureData = fd))
 
   if (.hasSlot(classifier, "gene_id_type")) {
     classifier_gene_id_type <- classifier@gene_id_type

diff --git a/R/train_cell_classifier.R b/R/train_cell_classifier.R
@@ -146,9 +146,9 @@ train_cell_classifier <- function(cds,
     sf <- pData(cds)$Size_Factor
     pd <- new("AnnotatedDataFrame", data = pData(cds))
     fd <- new("AnnotatedDataFrame", data = fData(cds))
-    cds <- newCellDataSet(as(exprs(cds), "dgCMatrix"),
+    cds <- suppressWarnings(newCellDataSet(as(exprs(cds), "dgCMatrix"),
                           phenoData = pd,
-                          featureData = fd)
+                          featureData = fd))
     pData(cds)$Size_Factor <- sf
   }
 
@@ -161,8 +161,8 @@ train_cell_classifier <- function(cds,
   fd <- new("AnnotatedDataFrame", data = fData(cds))
   temp <- exprs(cds)
   temp@x <- temp@x / rep.int(pData(cds)$Size_Factor, diff(temp@p))
-  norm_cds <- newCellDataSet(temp,
-                             phenoData = pd, featureData = fd)
+  norm_cds <- suppressWarnings(newCellDataSet(temp,
+                             phenoData = pd, featureData = fd))
   orig_cds <- cds
   if(cds_gene_id_type != classifier_gene_id_type)  {
     norm_cds <- cds_to_other_id(norm_cds, db=db, cds_gene_id_type,

diff --git a/R/utils.R b/R/utils.R
@@ -29,11 +29,11 @@ cds_to_other_id <- function(cds,
 
   pd = new("AnnotatedDataFrame", data = pData(cds))
   fd = new("AnnotatedDataFrame", data = fdata)
-  cds = newCellDataSet(matrix,
+  cds = suppressWarnings(newCellDataSet(matrix,
                        phenoData=pd,
                        featureData=fd,
                        expressionFamily=cds@expressionFamily,
-                       lowerDetectionLimit=cds@lowerDetectionLimit)
+                       lowerDetectionLimit=cds@lowerDetectionLimit))
 
   return(cds)
 }
@@ -270,9 +270,9 @@ check_markers <- function(cds,
   if (!is(exprs(cds), "dgCMatrix")) {
     pd <- new("AnnotatedDataFrame", data = pData(cds))
     fd <- new("AnnotatedDataFrame", data = fData(cds))
-    cds <- newCellDataSet(as(exprs(cds), "dgCMatrix"),
+    cds <- suppressWarnings(newCellDataSet(as(exprs(cds), "dgCMatrix"),
                           phenoData = pd,
-                          featureData = fd)
+                          featureData = fd))
     pData(cds)$Size_Factor <- sf
   }
 
@@ -291,8 +291,8 @@ check_markers <- function(cds,
   orig_cds <- cds
   temp <- exprs(cds)
   temp@x <- temp@x / rep.int(pData(cds)$Size_Factor, diff(temp@p))
-  cds <- newCellDataSet(temp,
-                        phenoData = pd, featureData = fd)
+  cds <- suppressWarnings(newCellDataSet(temp,
+                        phenoData = pd, featureData = fd))
 
   pData(cds)$Size_Factor <- sf
 
@@ -477,8 +477,6 @@ check_marker_conversion <- function(parse_list,
                                           marker_file_gene_id_type,
                                           cds_gene_id_type)
     bad_convert <- sum(is.na(gene_table$fgenes))
-  } else {
-    gene_table$cds <- gene_table$fgenes
   }
 
   gene_table$in_cds <- gene_table$fgenes %in% possible_genes