View source for 1D NMR Processing in Linux and Windows Example Script

    '''%Load MVAPACK'''   
     addpath('/opt/mvapack/'); %%This could also be used as 'pkg load mvapack' on systems where mvapack is installed

    '''%Load Data''' 
     F.dirs = glob('???');
     [F.data, F.parms, F.t] = loadnmr(F.dirs);

    '''%Add Classes and Labels''' 
     cls.Y = classes([7,8,6,8,8,8,7,8,7,8,8,8,8,8,8]);
     cls.labels = {'1','2','3','4','5','6','7','8','9','10','11','12','13','14','15'};

    '''%Zerofills'''
     F.data = zerofill(F.data, F.parms, 2); #number of zerofills can be adjusted

    '''%Build the Spectra/FT'''
     [S.data, S.ppm] = nmrft(F.data, F.parms);
     %Note: Check out the Quality (spit out a couple plots)
     plot(S.ppm,S.data(1,:)) %%  <-- Change 1 to a different number to inspect that spectrum.

    '''%Autophase the Spectra'''
     %Note, some users run this ~2-3 times for convergence
     [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms); 
     [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms); 
     [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms); 

    '''%Extract the Real Spectral Components'''
     XF.data = realnmr(S.data, F.parms);
     XF.ppm = S.ppm;

    '''%Check Plot to Find Reference Standard'''
     plot(XF.ppm, XF.data)

    '''%Reference Adjustment'''
     XF.ppm = refadj(XF.ppm, -0.160, 0.0);

    '''%Icoshift'''
     XF.data = icoshift(XF.data, XF.ppm);

    '''%Remove Undesired Regions''' 
     %Note:Removes all values between r0 and r1, r2 and r3, etc.
     r0= findnearest(XF.ppm, min(XF.ppm));
     r1=findnearest(XF.ppm, 0.4);
     r2=findnearest(XF.ppm, 0.97);
     r3=findnearest(XF.ppm, 1.33); 
     r4=findnearest(XF.ppm, 4.5);
     r5=findnearest(XF.ppm, 5.2);
     r6=findnearest(XF.ppm, 8.5);
     r7=findnearest(XF.ppm, max(XF.ppm));
     X.rm.var = [r7:r6,r5:r4,r3:r2,r1:r0];
     [XF.data, XF.ppm] = rmvar(XF.data, XF.ppm, X.rm.var);

    '''%Normalize Data'''
     X1.data= pqnorm(XF.data);
     X1.ppm=XF.ppm

    '''%Binning'''
     [B.data, B.ppm, B.widths]=binadapt(XF.data,XF.ppm,F.parms);

== Build Models ==

    '''% ''Principle Component Analysis'' '''
     mdlpca= pca(X1.data); 
     mdlpca = addclasses(mdlpca, cls.Z);

    '''% ''Plot Scores'' ''' 
     scoresplot(mdlpca, 2, [], true);
     print -deps -color 'FB-2-mdlPCA.eps'
     print -dpdf -color 'Fb-2-mdlPCA.pdf'
   
    '''%RQ Plot'''
     rqplot(mdlpca)
     print -deps -color 'FB-2-rqmdlPCA.eps'
     print -dpdf -color 'Fb-2-rqmdlPCA.pdf'
   
    '''%Save Scores'''
     savescores (mdlpca,FB-2-scoresPCA,3,cls.Y,cls.labels)


    '''% ''Orthogonal Projection to Latent Squares (OPLS)'' '''
     %Note: no seperation with binned data
     mdlopls = opls(X1.data, cls.Y);
     mdlopls = addlabels(mdlopls, cls.labels);
     print -deps -color 'FB-2-mdlOPLS.eps'
     print -dpdf -color 'Fb-2-mdlOPLS.pdf'
   
   

  '''%Validation Stages for OPLS Models'''
  

    '''%RQ Plot'''
     rqplot(mdlopls);
   

    '''%Permutation Test'''
     mdl.cv.perm = permtest(mdlopls);
     permscatter(mdl.cv.perm) 
  

    '''%CV Anova'''
     mdl.cv.anova = cvanova(mdlopls);
     mdl.cv.anova <!-- is this supposed to display the anova matrix? not really sure what this value is I guess-->

[[category:Needs_Updating|NMR Processing]] <!--Add in downloadable file for this script-->
[[category:Data_Processing_and_Analysis|NMR Processing]]