extract_spectra: Extract full MS2 spectra.

R/api.R

@@ -374,24 +374,22 @@ extr_data <-function(m) {
                            idx=integer(0),
                            rt=numeric(0),
                            intensity=numeric(0))
+    
+    spectra = empty_spectra_table()
+                         
     for (fn in names(lfdata)) {
-        ## x = lfdata[[fn]]$ms2[cgram_ms1,
-        ##                      .(an,
-        ##                        ce,
-        ##                        precid=i.precid,
-        ##                        rt,
-        ##                        intensity),
-        ##                      on=c(prec_idx="idx"),
-        ##                      nomatch=NULL,
-        ##                      allow.cartesian=T]
         rtab = relate_ms2_to_precid(coarse=coarse,ms2=lfdata[[fn]]$ms2,cgram_ms1=cgram_ms1)
+        sptab = extract_spectra(lms[[fn]],rtab)
         cgram_ms2 = rbind(cgram_ms2,rtab)
+        spectra = rbind(spectra,sptab)
     }
     setkey(cgram_ms1,precid,rt)
     setkey(cgram_ms2,precid,ce,rt)
+    setkey(spectra,precid,scan)
     m$db$extr$cgm$ms1 = cgram_ms1
     m$db$extr$cgm$ms2 = cgram_ms2
-    browser()
+    m$db$extr$spectra = spectra
+
     m
 
 }

R/data-model.R

@@ -103,3 +103,13 @@ make_db_precursors <- function(m) {
     m$db$precursors = masses
     m
 }
+
+
+empty_spectra_table <- function() {
+    r = data.table(precid=integer(0),
+                   scan=character(0),
+                   mz=numeric(0),
+                   intensity=numeric(0))
+    setkey(r,precid,scan)
+    r
+}

R/extraction.R

@@ -700,8 +700,19 @@ get_fdata <- function(ms) {
 
 
 relate_ms2_to_precid <- function(coarse,ms2,cgram_ms1) {
+    ## Take `coarse' table (the one with coarse mass limits), ms2
+    ## fData and ms1 chromatogram, then relate precids from cgram_ms1
+    ## to ms2 data.
+
+    ## Select those MS2 entries the parents of which coarsely match
+    ## compound lists masses.
     res = ms2[coarse,on=.(prec_mz>iso_coarse_min,prec_mz<iso_coarse_max),.(prec_mz=x.prec_mz,precid,prec_idx,scan,idx,ce,rt,intensity),nomatch=NULL]
     setkey(res,precid,prec_idx)
+
+    ## Now, make sure those coarsely matched MS2 actually have a
+    ## parent that finely matches something in the chromatogram (and
+    ## this is by ensuring that a `precid' with the correct scan (idx)
+    ## shows up in the chromatogram.
     cgram_ms1[res,on=.(precid,idx==prec_idx),
               .(precid,ce,scan=i.scan,
                 idx=i.idx,rt=i.rt,
@@ -709,3 +720,21 @@ relate_ms2_to_precid <- function(coarse,ms2,cgram_ms1) {
     
 }
 
+extract_spectra <- function(ms,cgram_ms2) {
+    ## This will extract full MS2 spectra based on ms2 chromatogram entries.
+    indices = cgram_ms2[,.SD,.SDcol=c("precid","scan","idx")]
+
+    res = empty_spectra_table()
+    selind = indices[,unique(.SD),.SDcol=c("scan","idx")]
+    sel = ms[selind$idx]
+
+    masses = mz(sel)
+    intensities = intensity(sel)
+    res = selind
+    setkey(res,scan)
+    res = res[,data.table(mz=masses[[scan]],
+                          intensity=intensities[[scan]]),
+              keyby=c("scan")]
+    res[indices,on=.(scan),precid:=i.precid]
+    
+}