final change

Author: sgosline

build/mpnst/01_mpnst_get_omics.R

@@ -47,20 +47,20 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|>
 pdx_data<-manifest|>dplyr::select(common_name,starts_with("PDX"))|>
     left_join(pdx_samps)|>
     dplyr::select(improve_sample_id,common_name,model_type,RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')|>
-        subset(!is.na(improve_sample_id)
+        subset(!is.na(improve_sample_id))
 
 tumor_data<- manifest|>dplyr::select(common_name,starts_with("Tumor"))|>
     left_join(tumor_samps)|>
     dplyr::select(improve_sample_id,common_name,model_type,RNASeq='Tumor_RNASeq',Mutations='Tumor_Somatic_Mutations',CopyNumber='Tumor_CNV')|>
     mutate(Proteomics='')|>
-    subset(!is.na(improve_sample_id)
+    subset(!is.na(improve_sample_id))
            ##we dont have tumor proteomics from these samples
 #print(tumor_data)
 
 mt_data<- manifest|>dplyr::select(common_name,starts_with("PDX"))|>
     left_join(mt_samps)|>
     dplyr::select(improve_sample_id,common_name,model_type, RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')|>##we dont have mt data yet, so collecting PDX instead
-    subset(!is.na(improve_sample_id)
+    subset(!is.na(improve_sample_id))
 #print(tumor_data)