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cGlycoTest.m
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cGlycoTest.m
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%% This is the test file for cGlyco with examples for Bcells and Monocytes.
%% To run this program, simply change the rootdir depending on the location of the installation directory of cGlyco
%% Then step throught the program to execute individual program modules
%% Define the root path of the cGlyco
rootdir = 'C:\Work\cGlyco';
%% Other dir
Bcelldir = fullfile(rootdir,'Testcase\Bcell');
Monocytesdir = fullfile(rootdir,'Testcase\Monocytes');
CompDir = fullfile(rootdir,'Testcase\BcellMonocytes');
colormapdir = fullfile(rootdir,'func');
%% Step 1 test case - Peak list generation
% B cell
[MSdata,fitPara]=peakList('Bcell_Human','dir',Bcelldir);
%% Step 2 test case - database building
% N-linked glycan
antennalib = {'';... % define all possible form of antennas here 1
'GlcNAc(b1-?)';... % 2
'Gal(b1-4)GlcNAc(b1-?)';... % 3
'Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-?)';... % 4
'NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-?)';... % 5
'NeuAc(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-?)';... % 6
'Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)';... % 7
'Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)';... % 8
'NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)';... % 9
'NeuAc(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)'}; % 10
coreStruct ='core4';
BranchType ='tetra';
withLinkage = 1;
outputdir = Bcelldir;
highmannose = 1;
GlyType = 'N-';
[glycanDB,outputname,LibSize] = genGlyLib(antennalib,coreStruct,withLinkage,outputdir,GlyType,BranchType,highmannose);
% O-linked glycan
antennalib = {'';... % define all possible form of antennas here 1
'NeuAc(a2-?)';... % 2
'Gal(b1-4)GlcNAc(b1-?)';... % 3
'Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-?)';... % 4
'NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-?';... % 5
'NeuAc(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-?)';... % 6
'Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)';... % 7
'Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)';... % 8
'NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)';... % 9
'NeuAc(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-?)'}; % 10
coreStruct = 'core1';
withLinkage = 1;
outputdir = Bcelldir;
GlyType = 'O-';
[glycanDB,outputname,LibSize] = genGlyLib(antennalib,coreStruct,withLinkage,outputdir,GlyType);
%% Step 3 test case - MS abundance
% B cell
MSDataFileName = 'Bcell_Human';
MSdir = Bcelldir;
glycanDBName = 'BcellglycanDB';
glycnDBdir = Bcelldir;
OverSegFilter = 1.5;
outputExcel = 'B_cell';
outputdir = Bcelldir;
[newglycanDB,outputfilename] = glycanAbundance(MSDataFileName,glycanDBName,MSdir,glycnDBdir,OverSegFilter,outputExcel,outputdir);
%% Step 4 test case - MS analysis
% listOfStruct
listOfStruct = {'LeX','sialylLeX','LacNAc','Sia_LacNAc','Bisecting','coreFuc'};
% B cell
MSfilename = 'Bcell';
glycanDB = 'Bcell_HumanglycanDB';
glycanDBdir = Bcelldir;
outputdir = Bcelldir;
newglycanDB = classification(MSfilename,glycanDB,glycanDBdir,outputdir,listOfStruct);
%% Comparison analysis
% listOfStruct
listOfStruct = {'LeX','sialylLeX','LacNAc','Sia_LacNAc','Bisecting','coreFuc'};
% Bcell
glycanDB = fullfile(Bcelldir,'Bcell_HumanglycanDB.mat');
load(glycanDB,'newglycanDB');
ResidueResult = MSResidueAnalysisGNAT('Bcell',newglycanDB);
% Save results to BcellMonocytes folder
storedir = fullfile(CompDir,'BcellResidue.mat');
save(storedir,'ResidueResult');
StructResult = MSStructAnalysisGNAT('Bcell',newglycanDB,listOfStruct);
% Save results to BcellMonocytes folder
storedir = fullfile(CompDir,'BcellStruct.mat');
save(storedir,'StructResult');
% Monocytes
glycanDB = fullfile(Monocytesdir,'Monocytes_HumanglycanDB.mat');
load(glycanDB,'newglycanDB');
ResidueResult = MSResidueAnalysisGNAT('Monocytes',newglycanDB);
% Save results to BcellMonocytes folder
storedir = fullfile(CompDir,'MonocytesResidue.mat');
save(storedir,'ResidueResult');
StructResult = MSStructAnalysisGNAT('Monocytes',newglycanDB,listOfStruct);
% Save results to BcellMonocytes folder
storedir = fullfile(CompDir,'MonocytesStruct.mat');
save(storedir,'StructResult');
% Comparison
ResidueMSFileList = {'BcellResidue','MonocytesResidue'};
StructMSFileList = {'BcellStruct','MonocytesStruct'};
outputfilename = 'Bcell_Monocytes';
[ResidueTypeExist,StructTypeExist] = Plotheatmap(ResidueMSFileList,StructMSFileList,outputfilename,CompDir,colormapdir,CompDir);
% Structure heatmap
glycanDB1 = 'Bcell_HumanglycanDB';
glycanDB2 = 'Monocytes_HumanglycanDB';
loadpath = CompDir;
storedir = CompDir;
PlotheatmapStruct(glycanDB1,glycanDB2,loadpath,colormapdir,storedir)