messar fix

daniellyz · Apr 11, 2021 · 28d70b6 · 28d70b6
1 parent f4afc9d
commit 28d70b6
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/R/average_spectrum.r b/R/average_spectrum.r
@@ -37,11 +37,9 @@ average_spectrum<-function(splist, mz_window = 0.01){
   #################################################
   ### Combine and average m/z with the same label##
   #################################################
-
-  print(N_feature)
-  print(NBS)
-  #I_matrix = matrix(0,N_feature,NBS) # Intensity matrix N_feature x Nb of spectra
-  I_matrix <- big.matrix(N_feature, NBS, type='integer', init=0)
+
+  I_matrix = matrix(0,N_feature,NBS) # Intensity matrix N_feature x Nb of spectra
+  #I_matrix <- big.matrix(N_feature, NBS, type='integer', init=0)
 
   avg_mzlist=rep(0,N_feature) # Averaged mass list
   #dev_matrix = matrix(0,N_feature,NBS)

diff --git a/R/process_lib2network.R b/R/process_lib2network.R
@@ -132,10 +132,12 @@ process_lib2network<-function(input_library, networking = T, polarity = c("Posit
 
         tmp_sp = splist[[i]]
         tmp_prec = metadata$PEPMASS[i]
-        tmp_messar = library_messar(query_spectrum = tmp_sp, params.query.sp = list(prec_mz = tmp_prec, use_prec = T, compound.type = "Metabolite"))
+        tmp_messar1 = library_messar(query_spectrum = tmp_sp, params.search = list(mz_search = 0.01, tops = 2), params.query.sp = list(prec_mz = tmp_prec, use_prec = T, compound.type = "Metabolite"))
+        tmp_messar2 = library_messar(query_spectrum = tmp_sp, params.search = list(mz_search = 0.01, tops = 2), params.query.sp = list(prec_mz = tmp_prec, use_prec = T, compound.type = "Drug"))
+        tmp_messar = rbind(tmp_messar1, tmp_messar2)
 
         if (!is.null(tmp_messar[,1])){
-          messar_output[[i]] = tmp_messar[,1]
+          messar_output[[i]] = unique(tmp_messar[,1])
         } else {messar_output[[i]] = "0"}
       }