Changes for revision.

cheeyeelim · b1804a02f14c3f5b4fb0c27381ba42e6a281a64d · cheeyeelim committed Mar 16, 2016 · Mar 16, 2016 · b1804a0
1 parent 67d8894
commit b1804a02f14c3f5b4fb0c27381ba42e6a281a64d
Unified Split

Showing with 420 additions and 328 deletions.

+3 −6 bon_wilsonrnaseq_hsc.R

+238 −158 gnw_bnlearn_btr_scoring.R

+22 −7 gnw_btr_model_inference.R

+154 −151 gnw_comparison_network_inference.R

+3 −6 krum_wilson_grow_hsc.R
diff --git a/bon_wilsonrnaseq_hsc.R b/bon_wilsonrnaseq_hsc.R
@@ -2,7 +2,7 @@
 library(BTR)
 library(doParallel)
 
-path='~/bool_final/'
+path='~/btr_output/'
 setwd(path)
 
 #Setting up for parallel processing.
@@ -20,14 +20,11 @@ bmodel = initialise_model(bon_bmodel)
 istate = initialise_data(bon_istate)
 
 #(3)Filtering expression data.
-tmp_data = initialise_raw_data(wilson_raw_rnaseq) #do not filter data at this stage. keep the whole matrix.
-cdata = tmp_data[[1]] #continuous data
-ddata = tmp_data[[2]] #discretised data
+cdata = initialise_raw_data(wilson_raw_rnaseq) #do not filter data at this stage. keep the whole matrix.
 fcdata = cdata[grepl('hsc', rownames(cdata)),] #select only HSC cells.
-fddata = ddata[grepl('hsc', rownames(ddata)),]
 
 #(3)Filtering expression data.
-result = model_train(cdata=fcdata, ddata=fddata, bmodel=bmodel, istate=istate, verbose=T)
+result = model_train(cdata=fcdata, bmodel=bmodel, istate=istate, verbose=T)
 
 filename = 'bon_wilson_rnaseq_HSC_trained_bmodel.rda'
 save(result, file=filename)