代谢组学富集分析kegg 功能富集MetaboAnalystR（R包 METABOSIGNAL ）

已于 2023-07-21 01:49:26 修改
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于 2023-07-06 01:11:38 首次发布
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代谢产物差异分析 | 生信菜鸟团http://www.bio-info-trainee.com/8512.html

 

step1 enrichment 富集分析部分 

 富集分析 smpd数据库 

# PID of current job: 1816221
mSet<-InitDataObjects("conc", "msetora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-SetCurrentMsetLib(mSet, "smpdb_pathway", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_0_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_0_", "png", 72, width=NA)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_1_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_1_", "png", 72, width=NA)
mSet<-SaveTransformedData(mSet)

 富集分析kegg数据库 

# PID of current job: 1893472
mSet<-InitDataObjects("conc", "msetora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-SetCurrentMsetLib(mSet, "kegg_pathway", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_0_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_0_", "png", 72, width=NA)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_1_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_1_", "png", 72, width=NA)
mSet<-SaveTransformedData(mSet)

富集分析Sub-class 

sub_class 注意单词的拼写

mSet<-SetCurrentMsetLib(mSet, "sub_class", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_3_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_3_", "png", 72, width=NA)
mSet<-PlotEnrichPieChart(mSet, "ora", "ora_pie_0_", "png", 72)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_4_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_4_", "png", 72, width=NA)
mSet<-PlotEnrichPieChart(mSet, "ora", "ora_pie_1_", "png", 72)
mSet<-SaveTransformedData(mSet)

smpdb  main_class

mSet<-InitDataObjects("conc", "msetora", FALSE)
cmpd.vec<-c("HMDB0001322","HMDB0005006","HMDB0013018","HMDB0033573","HMDB0037555","HMDB0038143","HMDB0043190","HMDB0044009","HMDB0045470","HMDB0251752","HMDB0257287","HMDB0257502","HMDB0257871","HMDB0263092","HMDB0280214","HMDB0290906","HMDB0291307","HMDB0293494","HMDB0293534","HMDB0293815","HMDB0001069","HMDB0004051","HMDB0008547","HMDB0012986","HMDB0015540","HMDB0015676","HMDB0033267","HMDB0033965","HMDB0035745","HMDB0036296","HMDB0038971","HMDB0039272","HMDB0042632","HMDB0055518","HMDB0056216","HMDB0061092","HMDB0115057","HMDB0116157","HMDB0247477","HMDB0247765","HMDB0248586","HMDB0248840","HMDB0249107","HMDB0249177","HMDB0249524","HMDB0249749","HMDB0250606","HMDB0252329","HMDB0252999","HMDB0253546","HMDB0254101","HMDB0254359","HMDB0254424","HMDB0256376","HMDB0257120","HMDB0257574","HMDB0258261","HMDB0260089","HMDB0281985","HMDB0294368","HMDB0303433","HMDB0303683","HMDB0304366","HMDB0029507","HMDB0244744","HMDB0252958","HMDB0252982","HMDB0253112","HMDB0256356","HMDB0257352","HMDB0000207","HMDB0031126","HMDB0035167","HMDB0035180","HMDB0035445","HMDB0036295","HMDB0038117","HMDB0040714","HMDB0060158","HMDB0241035","HMDB0244604","HMDB0248617","HMDB0250196","HMDB0250586","HMDB0251900","HMDB0252401","HMDB0252592","HMDB0254025","HMDB0258296","HMDB0277261","HMDB0303193")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PerformDetailMatch(mSet, "HMDB0037555");
mSet<-GetCandidateList(mSet);
mSet<-PerformDetailMatch(mSet, "HMDB0293815");
mSet<-GetCandidateList(mSet);
mSet<-PerformDetailMatch(mSet, "HMDB0037555");
mSet<-GetCandidateList(mSet);
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-SetCurrentMsetLib(mSet, "smpdb_pathway", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-SetMetabolomeFilter(mSet, F);


mSet<-SetCurrentMsetLib(mSet, "main_class", 2);

mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_1_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_1_", "png", 72, width=NA)
mSet<-PlotEnrichPieChart(mSet, "ora", "ora_pie_0_", "png", 72)

mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_2_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_2_", "png", 72, width=NA)
mSet<-PlotEnrichPieChart(mSet, "ora", "ora_pie_1_", "png", 72)
mSet<-SaveTransformedData(mSet)

super_class 

# PID of current job: 3489344
mSet<-InitDataObjects("conc", "msetora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-SetCurrentMsetLib(mSet, "super_class", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_0_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_0_", "png", 72, width=NA)
mSet<-PlotEnrichPieChart(mSet, "ora", "ora_pie_0_", "png", 72)

mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_1_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_1_", "png", 72, width=NA)
mSet<-PlotEnrichPieChart(mSet, "ora", "ora_pie_1_", "png", 72)


mSet<-SetMetabolomeFilter(mSet, F);
mSet<-SetCurrentMsetLib(mSet, "drug", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_2_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_2_", "png", 72, width=NA)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_3_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_3_", "png", 72, width=NA)
mSet<-PrepareSifDownloads(mSet)
mSet<-SetMetabolomeFilter(mSet, F);


mSet<-SetCurrentMsetLib(mSet, "predicted", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_4_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_4_", "png", 72, width=NA)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_5_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_5_", "png", 72, width=NA)
mSet<-SetMetabolomeFilter(mSet, F);


mSet<-SetCurrentMsetLib(mSet, "location", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_6_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_6_", "png", 72, width=NA)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_7_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_7_", "png", 72, width=NA)
mSet<-SaveTransformedData(mSet)

#####通路分析

 

# PID of current job: 905071
mSet<-InitDataObjects("conc", "pathora", FALSE)
cmpd.vec<-c("ALL","HMDB0001322","HMDB0005006","HMDB0013018","HMDB0033573","HMDB0037555","HMDB0038143","HMDB0043190","HMDB0044009","HMDB0045470","HMDB0251752","HMDB0257287","HMDB0257502","HMDB0257871","HMDB0263092","HMDB0280214","HMDB0290906","HMDB0291307","HMDB0293494","HMDB0293534","HMDB0293815","HMDB0001069","HMDB0004051","HMDB0008547","HMDB0012986","HMDB0015540","HMDB0015676","HMDB0033267","HMDB0033965","HMDB0035745","HMDB0036296","HMDB0038971","HMDB0039272","HMDB0042632","HMDB0055518","HMDB0056216","HMDB0061092","HMDB0115057","HMDB0116157","HMDB0247477","HMDB0247765","HMDB0248586","HMDB0248840","HMDB0249107","HMDB0249177","HMDB0249524","HMDB0249749","HMDB0250606","HMDB0252329","HMDB0252999","HMDB0253546","HMDB0254101","HMDB0254359","HMDB0254424","HMDB0256376","HMDB0257120","HMDB0257574","HMDB0258261","HMDB0260089","HMDB0281985","HMDB0294368","HMDB0303433","HMDB0303683","HMDB0304366","HMDB0029507","HMDB0244744","HMDB0252958","HMDB0252982","HMDB0253112","HMDB0256356","HMDB0257352","HMDB0000207","HMDB0031126","HMDB0035167","HMDB0035180","HMDB0035445","HMDB0036295","HMDB0038117","HMDB0040714","HMDB0060158","HMDB0241035","HMDB0244604","HMDB0248617","HMDB0250196","HMDB0250586","HMDB0251900","HMDB0252401","HMDB0252592","HMDB0254025","HMDB0258296","HMDB0277261","HMDB0303193")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetKEGG.PathLib(mSet, "rno", "current")
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-CalculateOraScore(mSet, "rbc", "hyperg")
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-PlotKEGGPath(mSet, "Biosynthesis of unsaturated fatty acids",576, 480, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689756142292.png",576.0, 480.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1689756245682.png",576.0, 480.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1689756246506.png",593.0, 494.0, 102.91666666666666)
mSet<-RerenderMetPAGraph(mSet, "zoom1689756248854.png",576.0, 480.0, 100.0)
mSet<-SaveTransformedData(mSet)

 

# PID of current job: 781822
mSet<-InitDataObjects("conc", "pathora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")

mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetKEGG.PathLib(mSet, "rno", "current")
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-CalculateOraScore(mSet, "rbc", "hyperg")
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )

mSet<-SaveTransformedData(mSet)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",576, 480, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689754804669.png",576.0, 480.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",576, 480, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689754809845.png",576.0, 480.0, 100.0)
mSet<-SaveTransformedData(mSet)

############=联合分析 --联合通路分析

 metabolic pathways 

 

 

# PID of current job: 3936457
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738608119.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738617217.png",582.0, 504.0, 102.85714285714285)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738617785.png",588.0, 509.0, 103.87755102040816)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738618510.png",605.0, 524.0, 106.93877551020408)
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",NA, NA, "png", 300)
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",12, 12, "png", 300)
mSet<-SaveTransformedData(mSet)

基因和代谢物联合分析 

# PID of current job: 2977288
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "rno")
mSet<-SetOrganism(mSet, "rno")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "rno", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "rno", "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotPathSummary(mSet, T, "path_view_1_", "png", 72, width=NA, NA, NA )
mSet<-PlotKEGGPath(mSet, "Thiamine metabolism",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689751276101.png",566.0, 490.0, 100.0)
mSet<-SaveTransformedData(mSet)

蛋白和代谢物联合分析

# PID of current job: 3109015
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "rno")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "rno", "uniprot");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "rno", "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "alpha-Linolenic acid metabolism",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689828045728.png",566.0, 490.0, 100.0)
mSet<-SaveTransformedData(mSet)

or all pathways. 

# PID of current job: 3936457
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738608119.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738617217.png",582.0, 504.0, 102.85714285714285)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738617785.png",588.0, 509.0, 103.87755102040816)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738618510.png",605.0, 524.0, 106.93877551020408)
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",NA, NA, "png", 300)
mSet<-PlotKEGGPath(mSet, "Fatty acid degradation",12, 12, "png", 300)
mSet<-SaveTransformedData(mSet)
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "all", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_1_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "One carbon pool by folate",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1689738776279.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "One carbon pool by folate",566, 490, "png", NULL)
mSet<-SaveTransformedData(mSet)

 

 

# PID of current job: 164558
mSet<-InitDataObjects("conc", "msetora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-SetCurrentMsetLib(mSet, "kegg_pathway", 2);
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_2_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_2_", "png", 72, width=NA)
mSet<-CalculateHyperScore(mSet)
mSet<-PlotORA(mSet, "ora_3_", "net", "png", 72, width=NA)
mSet<-PlotEnrichDotPlot(mSet, "ora", "ora_dot_3_", "png", 72, width=NA)
mSet<-SaveTransformedData(mSet)
mSet<-PreparePDFReport(mSet, "guest8108257609163143447")

step2 通路富集

# PID of current job: 665556
mSet<-InitDataObjects("conc", "pathora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetKEGG.PathLib(mSet, "rno", "current")
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-CalculateOraScore(mSet, "rbc", "hyperg")
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-PlotKEGGPath(mSet, "Glycine, serine and threonine metabolism",576, 480, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688953688357.png",576.0, 480.0, 100.0)
# PID of current job: 325220
mSet<-InitDataObjects("conc", "pathora", FALSE)
cmpd.vec<-c("Acetoacetic acid","Beta-Alanine","Creatine","Dimethylglycine","Fumaric acid","Glycine","Homocysteine","L-Cysteine","L-Isolucine","L-Phenylalanine","L-Serine","L-Threonine","L-Tyrosine","L-Valine","Phenylpyruvic acid","Propionic acid","Pyruvic acid","Sarcosine")
mSet<-Setup.MapData(mSet, cmpd.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-SetKEGG.PathLib(mSet, "rno", "current")
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-CalculateOraScore(mSet, "rbc", "hyperg")
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-PlotKEGGPath(mSet, "Glycine, serine and threonine metabolism",576, 480, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952908953.png",576.0, 480.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",576, 480, "png", NULL)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",576, 480, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952917573.png",576.0, 480.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952920203.png",593.0, 494.0, 102.91666666666666)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952920919.png",610.0, 508.0, 105.83333333333333)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952921827.png",593.0, 494.0, 102.91666666666666)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952922353.png",587.0, 489.0, 101.875)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952922744.png",587.0, 489.0, 101.875)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952923406.png",605.0, 504.0, 105.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952923925.png",622.0, 518.0, 107.91666666666666)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952925601.png",656.0, 547.0, 113.95833333333334)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952926176.png",673.0, 561.0, 116.875)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952926641.png",679.0, 566.0, 117.91666666666667)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952927102.png",673.0, 561.0, 116.875)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952927512.png",667.0, 556.0, 115.83333333333334)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952928019.png",667.0, 556.0, 115.83333333333334)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952928524.png",667.0, 556.0, 115.83333333333334)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952929928.png",576.0, 480.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952931658.png",576.0, 480.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688952932945.png",576.0, 480.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",576, 480, "png", NULL)
mSet<-PlotKEGGPath(mSet, "Glycine, serine and threonine metabolism",576, 480, "png", NULL)
mSet<-SaveTransformedData(mSet)

step3 联合分析

Algeria selection

The topology analysis evaluates the potential importance of a particular molecule (a node) based on its position within a pathway. Degree Centrality measures the number of links that connect to a node. Betweenness Centrality measures the number of shortest paths from all nodes to all the others that pass through a given node. Closeness Centrality measures the overall distance from a given node to all other nodes.

For integration methods, there are two general approaches - tight integration by combining queries in which genes and metabolites are pooled into a single query and used to perform enrichment analysis within their "pooled universe" or loose integration by combining p values in which enrichment analysis is performed separately for genes and metabolites in their "individual universe", and then individual p-values are combined via weighted Z-tests. Moreover, there are three options for computing weights. Let's assume the pathway database contains a total of 100 pathways covering a total of 1000 metabolites and 4000 genes, respectively. Pathway A contains 5 compounds and 45 genes, while pathway B contains 20 compounds and 30 genes.

  • Unweighted or equal weights (i.e metabolite: 0.5, gene: 0.5);
  • Weights based on the overall proportion of each omics within the "universe" (i.e metabolite: 0.2, gene: 0.8 for all pathways);
  • Weights based on the pathway-level proportion within individual "pathway space" (i.e. pathway A - metabolite 0.1, gene 0.9; pathway B - metabolite 0.4, gene 0.6)
Note that combing p-values can only be applied to pathways that receive hits from both input types (genes + metabolites). For pathways with hits from only one input type, p values calculated from their individual universe will be used. In this case, combining p values can be viewed as adjusting the confidence level based on new evidence (i.e. input from another omics layer). If no new evidence is available, the current confidence level remains.

 

# PID of current job: 731548
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "rno")
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688954289011.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688954299369.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",566, 490, "png", NULL)
Prepare4TarIntegNetwork(mSetObj)
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_1_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955034900.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955042271.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955042752.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955043934.png",582.0, 504.0, 102.85714285714285)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955044379.png",588.0, 509.0, 103.87755102040816)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955044775.png",594.0, 514.0, 104.89795918367346)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955045222.png",611.0, 529.0, 107.9591836734694)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955045614.png",611.0, 529.0, 107.9591836734694)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955046351.png",594.0, 514.0, 104.89795918367346)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955047996.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Aminoacyl-tRNA biosynthesis",566, 490, "png", NULL)
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-SaveTransformedData(mSet)

step3.2 genes-compound

# PID of current job: 731548
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "rno")
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688954289011.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688954299369.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",566, 490, "png", NULL)
Prepare4TarIntegNetwork(mSetObj)
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_1_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955034900.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955042271.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955042752.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955043934.png",582.0, 504.0, 102.85714285714285)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955044379.png",588.0, 509.0, 103.87755102040816)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955044775.png",594.0, 514.0, 104.89795918367346)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955045222.png",611.0, 529.0, 107.9591836734694)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955045614.png",611.0, 529.0, 107.9591836734694)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955046351.png",594.0, 514.0, 104.89795918367346)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955047996.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Aminoacyl-tRNA biosynthesis",566, 490, "png", NULL)
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-SaveTransformedData(mSet)
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_2_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Glycerophospholipid metabolism",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955277384.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Glycerophospholipid metabolism",566, 490, "png", NULL)
mSet<-SaveTransformedData(mSet)

 

# PID of current job: 731548
mSet<-InitDataObjects("conc", "pathinteg", FALSE)
mSet<-SetOrganism(mSet, "rno")
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688954289011.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688954299369.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Phenylalanine, tyrosine and tryptophan biosynthesis",566, 490, "png", NULL)
Prepare4TarIntegNetwork(mSetObj)
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_1_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955034900.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955042271.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955042752.png",566.0, 490.0, 100.0)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955043934.png",582.0, 504.0, 102.85714285714285)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955044379.png",588.0, 509.0, 103.87755102040816)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955044775.png",594.0, 514.0, 104.89795918367346)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955045222.png",611.0, 529.0, 107.9591836734694)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955045614.png",611.0, 529.0, 107.9591836734694)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955046351.png",594.0, 514.0, 104.89795918367346)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955047996.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Aminoacyl-tRNA biosynthesis",566, 490, "png", NULL)
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-SaveTransformedData(mSet)
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_2_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Glycerophospholipid metabolism",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955277384.png",566.0, 490.0, 100.0)
mSet<-PlotKEGGPath(mSet, "Glycerophospholipid metabolism",566, 490, "png", NULL)
mSet<-SaveTransformedData(mSet)
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "symbol");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "hmdb");
mSet<-CreateMappingResultTable(mSet)
mSet<-PrepareIntegData(mSet);
mSet<-PerformIntegPathwayAnalysis(mSet, "dc", "hyper", "integ", "query");
mSet<-PlotPathSummary(mSet, F, "path_view_3_", "png", 72, width=NA, NA, NA )
mSet<-CreateIntegMatchingTable(mSet);
mSet<-PlotKEGGPath(mSet, "Valine, leucine and isoleucine biosynthesis",566, 490, "png", NULL)
mSet<-RerenderMetPAGraph(mSet, "zoom1688955496924.png",566.0, 490.0, 100.0)
mSet<-SaveTransformedData(mSet)

step4 

 

# PID of current job: 1444258
mSet<-InitDataObjects("conc", "network", FALSE)
mSet<-SetOrganism(mSet, "hsa")
geneListFile<-"replace_with_your_file_name"
geneList<-readChar(geneListFile, file.info(geneListFile)$size)
mSet<-PerformGeneMapping(mSet, geneList, "hsa", "entrez");
cmpdListFile<-"replace_with_your_file_name"
cmpdList<-readChar(cmpdListFile, file.info(cmpdListFile)$size)
mSet<-PerformCmpdMapping(mSet, cmpdList, "hsa", "kegg");
mSet<-CreateMappingResultTable(mSet)
mSet<-GetNetworkGeneMappingResultTable(mSet)
mSet<-PrepareNetworkData(mSet);
mSet<-PrepareKeggQueryJson(mSet)
mSet<-PerformKOEnrichAnalysis_KO01100(mSet, "pathway", "network_enrichment_pathway_0");
mSet<-SearchNetDB(mSet, "pheno", "gene_metabolites", FALSE, 0.5)
mSet<-CreateGraph(mSet)
mSet<-SaveTransformedData(mSet)
Specify analysis parameters:

Algorithms

Mummichog
P-value cutoff: (default top 10% peaks)

GSEA(using the overall rank based on t.score)
Visual analytics:

Scatter plot - test significant peaks

Heatmaps - test peaks in a visual pattern (good for multiple groups)

Advanced options   
Edit Currency Metabolites
Edit Adducts
Select a pathway library:(KEGG pathway info were obtained in Oct. 2019)

Mammals

Homo sapiens (human) [MFN]

Homo sapiens (human) [BioCyc]

Homo sapiens (human) [KEGG]

Mus musculus (mouse) [BioCyc]

Mus musculus (mouse) [KEGG]

Rattus norvegicus (rat) [KEGG]

Bos taurus (cow) [KEGG]
Birds

Gallus gallus (chicken) [KEGG]
Fish

Danio rerio (zebrafish) [KEGG]

Danio rerio (zebrafish) [MTF]

Insects

Drosophila melanogaster (fruit fly) [KEGG]

Drosophila melanogaster (fruit fly) [BioCyc]
Nematodes

Caenorhabditis elegans (nematode) [KEGG]
Fungi

Saccharomyces cerevisiae (yeast) [KEGG]

Saccharomyces cerevisiae (yeast) [BioCyc]
Plants

Oryza sativa japonica (Japanese rice) [KEGG]

Arabidopsis thaliana (thale cress) [KEGG]
Parasites

Schistosoma mansoni [KEGG]

Plasmodium falciparum 3D7 (Malaria) [KEGG]

Trypanosoma brucei [KEGG]
Prokaryotes

Escherichia coli K-12 MG1655 [KEGG]

Bacillus subtilis [KEGG]

Pseudomonas putida KT2440 [KEGG]

Staphylococcus aureus N315 (MRSA/VSSA) [KEGG]

Thermotoga maritima [KEGG]

Synechococcus elongatus PCC7942 [KEGG]

Mesorhizobium japonicum MAFF 303099 [KEGG]
Metabolite Sets

Lipids - Main Chemical Class

Lipids - Sub Chemical Class

Non-Lipids - Main Chemical Class

Non-Lipids - Sub Chemical Class

Disease-associated Metabolite Sets (Blood)

Disease-associated Metabolite Sets (CSF)

Disease-associated Metabolite Sets (Urine)

SNP-associated Metabolite Sets

Location-based Metabolite Sets

Predicted Metabolite Sets

MetaboSignal2.knit

使用MetaboDiff包分析非靶向代谢组数据 - 简书最近手里有个非靶向代谢组的数据，通过学习MetaboDiff包来熟悉代谢组分析的思路和流程，接下来的流程来自于MetaboDiff包官方帮助文档。 1. MetaboDiff...https://www.jianshu.com/p/80af83c2f630https://www.metaboanalyst.ca/docs/RTutorial.xhtmlhttps://www.metaboanalyst.ca/docs/RTutorial.xhtmlhttps://www.metaboanalyst.ca/docs/APIs.xhtml

物尽其用｜最全的HMDB数据库使用教程在这里

    The different options for input.type are given below:
        name - Compound name (e.g., 1,3-Diaminopropane)
        hmdb - Human Metabolome Database (e.g., HMDB0000002)
        pubchem - PubChem Substance and Compound databases(e.g., 428)
        chebi - Chemical Entities of Biological Interest(e.g., 15725)
        metlin - Metabolite and Chemical Entity Database (e.g., 5081)
        kegg - KEGG COMPOUND Database (e.g., C00986)

https://drive.google.com/file/d/1bLHQC8G7n9XyBG4Vim63hhICb4Qtw36M/viewhttps://drive.google.com/file/d/1bLHQC8G7n9XyBG4Vim63hhICb4Qtw36M/view

2.1 Over representation analysis
We will go over two analysis workflows, the first is when the input is a list to perform over representation

analysis. The first step is to create a vector containing a list of compound names. The list will then be cross-
referenced (CrossReferencing) against the MetaboAnalyst compound libraries (HMDB, PubChem, KEGG,

etc.), and any compounds without a hit will have NA. This step may take long due to downloading of libraries
if they do not already exist in your working directory.

InitDataObjects {MetaboAnalystR}

R Documentation

Constructs a dataSet object for storing data

Description

This functions handles the construction of a mSetObj object for storing data for further processing and analysis. It is necessary to utilize this function to specify to MetaboAnalystR the type of data and the type of analysis you will perform.

Usage

InitDataObjects(data.type, anal.type, paired=FALSE)

Arguments

data.type

The type of data, either list (Compound lists), conc (Compound concentration data), specbin (Binned spectra data), pktable (Peak intensity table), nmrpeak (NMR peak lists), mspeak (MS peak lists), or msspec (MS spectra data)

anal.type

Indicate the analysis module to be performed: stat, pathora, pathqea, msetora, msetssp, msetqea, mf, cmpdmap, smpmap, or pathinteg

paired

Indicate if the data is paired or not. Logical, default set to FALSE

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

==============================

CreateMappingResultTable {MetaboAnalystR}

R Documentation

Creates the mapping result table

Description

Creates the mapping result table

Usage

CreateMappingResultTable(mSetObj = NA)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

[Package MetaboAnalystR version 4.0.0 Index]

---------------==============================================

CrossReferencing {MetaboAnalystR}

R Documentation

Various functions for mapping b/w names & database identifiers Given a list of compound names or ids, find matched name or ids from selected databases

Description

Given a list of compound names or ids find matched name or IDs from selected databases

Usage

CrossReferencing(
  mSetObj = NA,
  q.type,
  hmdb = T,
  pubchem = T,
  chebi = F,
  kegg = T,
  metlin = F,
  lipid = F
)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects).

q.type

Input the query type, "name" for compound names, "hmdb" for HMDB IDs, "kegg" for KEGG IDs, "pubchem" for PubChem CIDs, "chebi" for ChEBI IDs, "metlin" for METLIN IDs, and "hmdb_kegg" for a both KEGG and HMDB IDs.

hmdb

Logical, T to cross reference to HMDB, F to not.

pubchem

Logical, T to cross reference to PubChem, F to not.

chebi

Logical, T to cross reference to CheBI, F to not.

kegg

Logical, T to cross reference to KEGG, F to not.

metlin

Logical, T to cross reference to MetLin, F to not.

lipid

Logical, if features are lipids (T), a different database will be used for compound matching.

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

========================================

PerformDetailMatch {MetaboAnalystR}
R Documentation

Perform detailed name match

Description

Given a query, perform compound matching.

Usage

PerformDetailMatch(mSetObj = NA, q)

Arguments

mSetObj

Input name of the created mSet Object.

q

Input the query.

===================

SetCandidate {MetaboAnalystR}R Documentation

Set matched name based on user selection from all potential hits

Description

Note: to change object in the enclosing enviroment, use "<<-"

Usage

SetCandidate(mSetObj = NA, query_nm, can_nm)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects).

query_nm

Input the query name.

can_nm

Input the candidate name.

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

 ====-------------

SetMetabolomeFilter {MetaboAnalystR}R Documentation

Set metabolome filter

Description

Set metabolome filter

Usage

SetMetabolomeFilter(mSetObj = NA, TorF)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

TorF

Input metabolome filter

-================

SetCurrentMsetLib {MetaboAnalystR}

R Documentation

Set current user selected metset library for search

Description

if enrichment analysis, also prepare lib by creating a list of metabolite sets

Usage

SetCurrentMsetLib(mSetObj=NA, libname, excludeNum)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

libname
Input user selected name of library, "self", "kegg_pathway", "smpdb_pathway", "blood", "urine", "csf", "snp", "predicted", "location", and "drug".
excludeNum

Users input the mimimum number compounds within selected metabolite sets (metabolitesets < excludeNum)

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL

-----------------------

CalculateHyperScore {MetaboAnalystR}R Documentation

Over-representation analysis using hypergeometric tests

Description

Over-representation analysis using hypergeometric tests The probability is calculated from obtaining equal or higher number of hits using 1-phyper. Since phyper is a cumulative probability, to get P(X>=hit.num) => P(X>(hit.num-1))

Usage

CalculateHyperScore(mSetObj = NA)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

====================

PlotORA {MetaboAnalystR}R Documentation

Plot over-representation analysis (ORA)

Description

Plot over-representation analysis (ORA)

Usage

PlotORA(mSetObj=NA, imgName, imgOpt, format="png", dpi=72, width=NA)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

imgName

Input a name for the plot

imgOpt

"net"

format

Select the image format, "png", or "pdf".

dpi

Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images, the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.

width

Input the width, there are 2 default widths, the first, width = NULL, is 10.5. The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.

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