diff --git a/DESCRIPTION b/DESCRIPTION
index c100a03..d1d39d5 100644
--- 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 = "hpliner@uw.edu", role = c("aut", "cre")), 
     person("Cole", "Trapnell", email = "coletrap@uw.edu", role = c("aut")))
diff --git a/NAMESPACE b/NAMESPACE
index 9504e89..ff7b80d 100644
--- 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
index 30763d8..413eb13 100644
--- 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
index ee45823..6ff1acb 100644
--- a/man/check_markers.Rd
+++ b/man/check_markers.Rd
@@ -6,7 +6,7 @@
 \usage{
 check_markers(cds, marker_file, db, cds_gene_id_type = "SYMBOL",
   marker_file_gene_id_type = "SYMBOL", propogate_markers = TRUE,
-  use_tf_idf = TRUE)
+  use_tf_idf = TRUE, classifier_gene_id_type = "ENSEMBL")
 }
 \arguments{
 \item{cds}{Input CDS object.}
@@ -32,6 +32,10 @@ generally be \code{TRUE}.}
 \item{use_tf_idf}{Logical. Should TF-IDF matrix be calculated during
 estimation? If \code{TRUE}, estimates will be more accurate, but
 calculation is slower with very large datasets.}
+
+\item{classifier_gene_id_type}{The type of gene ID that will be used in the
+classifier. If possible for your organism, this should be "ENSEMBL", which
+is the default.}
 }
 \value{
 Data.frame of marker check results.
diff --git a/man/garnett_classifier.Rd b/man/garnett_classifier.Rd
index 3227f70..8871d65 100644
--- a/man/garnett_classifier.Rd
+++ b/man/garnett_classifier.Rd
@@ -17,6 +17,7 @@ functions.
  \describe{
    \item{\code{classification_tree}:}{Object of class \code{"igraph"}}
    \item{\code{cell_totals}:}{Object of class \code{"numeric"}}
+   \item{\code{gene_id_type}:}{Object of class \code{"character"}}
    \item{\code{references}:}{Object of class \code{"list"}}
  }
 }
diff --git a/man/get_feature_genes.Rd b/man/get_feature_genes.Rd
index 046e4f9..1074c2d 100644
--- a/man/get_feature_genes.Rd
+++ b/man/get_feature_genes.Rd
@@ -14,7 +14,7 @@ get_feature_genes(classifier, node = "root", convert_ids = TRUE,
 \item{node}{Character. The name of the parent node of the multinomial
 classifier you would like to view features for. If top level, use "root".}
 
-\item{convert_ids}{Logical. Should ENSEMBL IDs be converted to SYMBOL?}
+\item{convert_ids}{Logical. Should classifier IDs be converted to SYMBOL?}
 
 \item{db}{Bioconductor AnnotationDb-class package for converting gene IDs.
 For example, for humans use org.Hs.eg.db. See available packages at
diff --git a/man/train_cell_classifier.Rd b/man/train_cell_classifier.Rd
index 057ed07..d141a15 100644
--- a/man/train_cell_classifier.Rd
+++ b/man/train_cell_classifier.Rd
@@ -7,7 +7,8 @@
 train_cell_classifier(cds, marker_file, db, cds_gene_id_type = "ENSEMBL",
   marker_file_gene_id_type = "SYMBOL", min_observations = 8,
   max_training_samples = 500, num_unknown = 500,
-  propogate_markers = TRUE, cores = 1, lambdas = NULL)
+  propogate_markers = TRUE, cores = 1, lambdas = NULL,
+  classifier_gene_id_type = "ENSEMBL")
 }
 \arguments{
 \item{cds}{Input CDS object.}
@@ -47,6 +48,10 @@ generally be \code{TRUE}.}
 \item{lambdas}{\code{NULL} or a numeric vector. Allows the user to pass
 their own lambda values to \code{\link[glmnet]{cv.glmnet}}. If \code{NULL},
 preset lambda values are used.}
+
+\item{classifier_gene_id_type}{The type of gene ID that will be used in the
+classifier. If possible for your organism, this should be "ENSEMBL", which
+is the default.}
 }
 \description{
 This function takes single-cell expression data in the form of a CDS object