genome_features_overlaps

R/genome_features_overlaps.R

@@ -219,9 +219,11 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat
     # remove tag
     annot[,tag:=NULL]
 
-    ###################
-    # merge with overlapped features
-    annot<-merge(annot,features@gff,by.x="tx_name",by.y="Name",all.x=T,sort=F)
+    if(base::ncol(features@gff)>1){
+      ###################
+      # merge with overlapped features
+      annot<-merge(annot,features@gff,by.x="tx_name",by.y="Name",all.x=T,sort=F)
+    }
 
     ###################
     # locate feature tag
@@ -241,7 +243,7 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat
 
     ###################
     # cast featurescount
-    features_count=dcast.data.table(features_count,
+    features_count=data.table::dcast(features_count,
     condition~feature_type,value.var="count")
 
     ###################
@@ -264,7 +266,7 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat
 
     ###################
     # format for plot
-    Data=melt.data.table(features_frequency,id.vars="condition",
+    Data=data.table::melt(features_frequency,id.vars="condition",
     variable.name = "feature", value.name = "frequency")
 
     ###################
@@ -338,7 +340,7 @@ setMethod("genome_features_overlaps",definition=function(peaks,features,figs_pat
 
       ###################
       # cast Data
-      Data<-dcast.data.table(Data,tag~feature_type,value.var="count")
+      Data<-data.table::dcast(Data,tag~feature_type,value.var="count")
 
       ###################
       # replace NA by 0