add utilisation_metaboanalystr

utilisation_metaboanalystr.R

+#library(devtools)
+
+:#devtools::install_github("xia-lab/MetaboAnalystR", build = TRUE, build_vignettes = FALSE)
+
+# Step 2: Install MetaboAnalystR with documentation
+#devtools::install_github("xia-lab/MetaboAnalystR", build = TRUE, build_vignettes = TRUE, build_manual =T)
+  
+library(MetaboAnalystR)
+
+tmp.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")
+
+# Create mSetObj
+mSet<-InitDataObjects("conc", "msetora", FALSE)
+
+mSet<-Setup.MapData(mSet, tmp.vec);
+
+mSet<-CrossReferencing(mSet, "name");
+
+
+mSet$name.map
+
+# Create the mapping results table
+mSet<-CreateMappingResultTable(mSet)
+
+# Input the name of the compound without any matches 
+mSet<-PerformDetailMatch(mSet, "L-Isolucine");
+
+# Create list of candidates to replace the compound
+mSet <- GetCandidateList(mSet);
+
+# Set the metabolite filter
+mSet<-SetMetabolomeFilter(mSet, F);
+
+# Select metabolite set library, refer to 
+mSet<-SetCurrentMsetLib(mSet, "smpdb_pathway", 0);
+
+# Calculate hypergeometric score, results table generated in your working directory
+mSet<-CalculateHyperScore(mSet)
+
+mSet<-PlotORA(mSet, "ora_0_", "bar", "png", dpi=300, width=NA)