08302024

V2.1/ODA/MetaboAnalyst_3.0.3/enrich_path_stats.R

@@ -31,7 +31,7 @@ CalculateOraScore1 <- function(mSetObj=NA, nodeImp, method){
   }
   q.size<-length(ora.vec);
 
-  if(is.na(ora.vec) || q.size==0) {
+  if(q.size==0) {	#Removed "|| is.na(ora.vec)" by ZZY on 7/31/24.
     if(mSetObj$pathwaylibtype == "KEGG"){
       AddErrMsg("No valid KEGG compounds found!");
     } else if(mSetObj$pathwaylibtype == "SMPDB"){

V2.1/ODA/MetaboAnalyst_3.0.3/enrich_stats.R

@@ -26,7 +26,7 @@ CalculateHyperScore1 <- function(mSetObj=NA){
 
   q.size<-length(ora.vec);
   
-  if(is.na(ora.vec) || q.size==0) {
+  if(q.size==0) {	#Removed "|| is.na(ora.vec)" by ZZY on 7/31/24.
     AddErrMsg("No valid HMDB compound names found!");
     return(0);
   }

V2.1/ODA/ODA.R

@@ -94,31 +94,32 @@ if (odaObj$attributes$nInterestedFeatures>0) {
 	rowOffset=rowOffset+odaObj$attributes$nInterestedFeatures+3
 	wbObj=writeTable(wbObj,'Selected_Features',odaObj$presentGroups[odaObj$features$interested,,drop=F],'Group_Counts',odaObj$featureDescription,rowOffset,0)
 
+}
+##############################End Writing Selected Features#####################################
+
 ##############################Begin MSEA-ORA Analysis by MetaboAnalyst#####################################
-	if (odaObj$parameters$oraMethod=='msea-ora'&&odaObj$parameters$eaDB!='no'&&!is.null(odaObj$features$eaMetabolites)) {
-		eaPath=file.path(odaObj$eaPath,paste0(odaObj$parameters$eaDB,'_MSEA-ORA'))
-		if (file.exists(eaPath)&&!rlang::is_empty(dir(eaPath))) {
-			stop('ORA folder is not empty.')
-		} else {
-			dir.create(eaPath,recursive=T,showWarnings=F)
-			MSEA_ORA(file.path(eaPath,'msea_ora'),rownames(odaObj$features$eaMetabolites),odaObj$features$refMetabolites,idType=odaObj$features$eaMetaboliteIDType,dbType=odaObj$parameters$eaDB,lipid=(odaObj$parameters$featureType=='lipid'),eaFile=odaObj$parameters$eaFile)
-		}
+if (odaObj$parameters$oraMethod=='msea-ora'&&odaObj$parameters$eaDB!='no'&&!is.null(odaObj$features$eaMetabolites)) {
+	eaPath=file.path(odaObj$eaPath,paste0(odaObj$parameters$eaDB,'_MSEA-ORA'))
+	if (file.exists(eaPath)&&!rlang::is_empty(dir(eaPath))) {
+		stop('ORA folder is not empty.')
+	} else {
+		dir.create(eaPath,recursive=T,showWarnings=F)
+		MSEA_ORA(file.path(eaPath,'msea_ora'),rownames(odaObj$features$eaMetabolites),odaObj$features$refMetabolites,idType=odaObj$features$eaMetaboliteIDType,dbType=odaObj$parameters$eaDB,lipid=(odaObj$parameters$featureType=='lipid'),eaFile=odaObj$parameters$eaFile)
 	}
+}
 ##############################End MSEA-ORA Analysis by MetaboAnalyst#####################################
 
 ##############################Begin MSPA-ORA Analysis by MetaboAnalyst#####################################
-	if (odaObj$parameters$oraMethod=='mspa-ora'&&odaObj$parameters$eaDB!='no'&&!is.null(odaObj$features$eaMetabolites)) {
-		eaPath=file.path(odaObj$eaPath,paste0(odaObj$parameters$eaDB,'_MSPA-ORA'))
-		if (file.exists(eaPath)&&!rlang::is_empty(dir(eaPath))) {
-			stop('ORA folder is not empty.')
-		} else {
-			dir.create(eaPath,recursive=T,showWarnings=F)
-			MSPA_ORA(file.path(eaPath,'mspa_ora'),rownames(odaObj$features$eaMetabolites),odaObj$features$refMetabolites,idType=odaObj$features$eaMetaboliteIDType,dbType=odaObj$parameters$eaDB,odaObj$parameters$species,eaFile=odaObj$parameters$eaFile)
-		}
+if (odaObj$parameters$oraMethod=='mspa-ora'&&odaObj$parameters$eaDB!='no'&&!is.null(odaObj$features$eaMetabolites)) {
+	eaPath=file.path(odaObj$eaPath,paste0(odaObj$parameters$eaDB,'_MSPA-ORA'))
+	if (file.exists(eaPath)&&!rlang::is_empty(dir(eaPath))) {
+		stop('ORA folder is not empty.')
+	} else {
+		dir.create(eaPath,recursive=T,showWarnings=F)
+		MSPA_ORA(file.path(eaPath,'mspa_ora'),rownames(odaObj$features$eaMetabolites),odaObj$features$refMetabolites,idType=odaObj$features$eaMetaboliteIDType,dbType=odaObj$parameters$eaDB,odaObj$parameters$species,eaFile=odaObj$parameters$eaFile)
 	}
-##############################End MSPA-ORA Analysis by MetaboAnalyst#####################################
 }
-##############################End Writing Selected Features#####################################
+##############################End MSPA-ORA Analysis by MetaboAnalyst#####################################
 
 ##############################Begin JointPA Analysis by MetaboAnalyst#####################################
 if ((!is.null(odaObj$features$eaMetabolites)||!is.null(odaObj$features$eaGenes))&&odaObj$parameters$jointPA!='no') {