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Graph-based time alignment algorithms for multiple LC-MS datasets
*Last updated: Nov 11 2013*
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File contained:
alignmentevaluation.cpp
alignmentevaluation.h
dtw.cpp
dtw.h
featuremap.cpp
featuremap.h
lowess.cpp
lowess.h
lwbmatch.cpp
lwbmatch.h
main.cpp
README
CMakeList.txt(*)
linux_lwbmatch.tar.gz
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Step 1: Download CMake(the cross-platform building system) from http://www.cmake.org/.
Step 2: Using CMake to generate native makefiles and workspaces:
example:
cmake -G "Unix Makefiles" PATH_OF_CMakeLists.txt or cmake -G "Visual Studio 10" PATH_OF_CMakeLists.txt or cmake -G "KDevelop3" PATH_OF_CMakeLists.txt
The list of IDEs(Integrated Development Environment) supported by CMake could be checked by "cmake --help"
**A package of unix makefile is attached."
Step 3: The usage of executable file "lwbmatch.exe" in Windows or "lwbmatch" in Linux
./lwbmatch methodID th_RT th_MZ th_intensity fileNum fileListPath outputPath gtPath separatePoint
Or
./lwbmatch methodID th_RT th_MZ th_intensity fileNum fileListPath outputPath
in Windows, change "./lwbmatch" to "lwbmatch.exe"
Example:
/LWBMatch/build/lwbmatch 1 500 0.2 1000000000 20 /evaluation/dataset/Standard_Protein_Mix_Database/Mix_4+Mix_7/FeatureXMLList /evaluation/result/Standard_Protein_Mix_Database/Mix_4+Mix_7/Mix_4+Mix_7_1.resu /evaluation/dataset/Standard_Protein_Mix_Database/Mix_4+Mix_7/Mix_4+Mix_7_GroundTruth.resu 10
Or
/LWBMatch/build/lwbmatch 1 500 0.2 1000000000 20 /evaluation/dataset/Standard_Protein_Mix_Database/Mix_4+Mix_7/FeatureXMLList /evaluation/result/Standard_Protein_Mix_Database/Mix_4+Mix_7/Mix_4+Mix_7_1.resu
methodID: 1 for LWBMatch, 2 for DTW
th_RT,th_MZ,th_intensity: tolerance
fileNum: the number of sample files
fileListPath: the path of the file containing all the sample files' paths
outputPath: the path of the file to store the alignment results
gtPath: the path of the file containing ground truth
separatePoint: separate point for combined datasets. For example, a combined dataset consists of 3 samples from the first dataset and 4 samples from second datasets,like A1 A2 A3 B1 B2 B3 B4, so the separate point is 3. This parameter is for heterogeneous alignment evaluation.
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How to generate FeatureMap:
Using tools attached to OpenMS:
FileConverter -in /dataset/Standard_Protein_Mix_Database/Mix_1/20060502data06.mzXML -in_type 'mzXML' -out /dataset/Standard_Protein_Mix_Database/Mix_1/20060502data06.tmp.mzML -out_type 'mzML'
FileFilter -in /dataset/Standard_Protein_Mix_Database/Mix_1/20060502data06.tmp.mzML -in_type 'mzML' -out /dataset/Standard_Protein_Mix_Database/Mix_1/20060502data06.mzML -out_type 'mzML' -int 10:
FeatureFinder -in /dataset/Standard_Protein_Mix_Database/Mix_1/20060502data06.mzML -out /dataset/Standard_Protein_Mix_Database/Mix_1/20060502data06.featureXML -type 'centroided'
All the functions can be found in OpenMS suite (Kohlbacher et al., 2007).
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Graph-based time alignment algorithms for multiple LC-MS datasets
*Last updated: Apr 16 2013*
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File contained:
alignmentevaluation.cpp
alignmentevaluation.h
dtw.cpp
dtw.h
featuremap.cpp
featuremap.h
lowess.cpp
lowess.h
lwbmatch.cpp
lwbmatch.h
main.cpp
README
CMakeList.txt(*)
----------------------------------------------------------------------------------------------------------------------------------
Step 1: Download CMake(the cross-platform building system) from http://www.cmake.org/.
Step 2: Using CMake to generate native makefiles and workspaces:
example:
cmake -G "Visual Studio 10" PATH_OF_CMakeLists.txt or cmake -G "KDevelop3" PATH_OF_CMakeLists.txt
The list of IDEs(Integrated Development Environment) supported by CMake could be checked by "cmake --help"
Step 3: The usage of executable file "lwbmatch.exe" in Windows or "lwbmatch" in Linux
lwbmatch.exe methodID th_RT th_MZ th_intensity fileNum fileListPath outputPath gtPath separatePoint
or
lwbmatch methodID th_RT th_MZ th_intensity fileNum fileListPath outputPath gtPath separatePoint
methodID: working function: 1 for LWBMatch, 2 for DTW
th_RT th_MZ th_intensity: tolerance
fileNum: the number of sample files
fileListPath: the path of the file containing all the sample files' paths
outputPath: the path of the file to store the alignment results
gtPath: the path of the file containing ground truth
separatePoint: separate point for combined datasets. For example, a combined dataset consists of 3 samples from
the first dataset and 4 samples from second datasets,like A1 A2 A3 B1 B2 B3 B4, so the separate
point is 3. This parameter is for heterogeneous alignment evaluation.
example:
/LWBMatch/build/lwbmatch 1 500 0.2 1000000000 20 /evaluation/dataset/Standard_Protein_Mix_Database/Mix_4+Mix_7/FeatureXMLList /evaluation/result/Standard_Protein_Mix_Database/Mix_4+Mix_7/Mix_4+Mix_7_1.resu /evaluation/dataset/Standard_Protein_Mix_Database/Mix_4+Mix_7/Mix_4+Mix_7_GroundTruth.resu 10
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