Add --all mode

.gitignore

@@ -2,6 +2,8 @@ Data/*
 test/*
 Results/*
 Results_R/*
+R_Packages/*
+all_sets_test/*
 rrintcc_BOOST
 rrintcc_BOOST.log
 *.o

READ.ME

@@ -50,5 +50,86 @@ plink1.9 --bfile MIGen_QC --recode --out MIGen_QC
 .frq file can be generated using plink1.9, e.g.
 plink1.9 --file MIGen_QC --freq --out MIGen_QC 
 plink1.9 --bfile MIGen_QC --freq --out MIGen_QC 
+
+
+******************************************************************
+4. Install R, Rcpp and RInside dependencies
+******************************************************************
+
+1). Need to install R base env
+sudo apt install r-base-core
+
+2). Also Need to install mvtnorm, Rcpp and RInside (The packages can be downloaded online)
+sudo R CMD INSTALL xxx.tar.gz
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configNames.txt

@@ -8,19 +8,22 @@
 # The first word in a line is the variable name in rrintcc
 # The second word in a line is the content for this variable 
 # Variables that need to be specified in this file:
-# foutpath, resname, logname, filename, mapname, setpath, setname
+# foutpath, resname, logname, filename, mapname, setname
+# setnumber, setpath (These two are only needed under --all/-a)
 #################################################################
 
-foutpath    Results/snp_results/
-resname	    Results/region_pair_results.txt
+foutpath    all_sets_test/Results/snp_results/
+resname	    all_sets_test/Results/region_pair_results.txt
 logname	    Results/rrintcc_BOOST.log
 
-filename    Data/filenamelist.txt
-mapname	    Data/example_bt_tag.map
+filename    all_sets_test/Data/filenamelist.txt
+mapname	    all_sets_test/Data/MIGen_QC.map
 setname	    Data/example_bt_tag.set
 
-# Format of .set/.snps names: locipair1/2/.../.set/snp
-setpath	    all_sets/
+# setpath is used for real data, so that we only read the BOOST data once 
+# in order to calculate the set pairs inside one run of rrintcc
+setpath	    all_sets_test/
+setnumber	3
 
 # mapname    CUHK_HKDRGWA_6445CC_Clean_Ch1-22.map
 

configNames_example.txt

@@ -8,7 +8,8 @@
 # The first word in a line is the variable name in rrintcc
 # The second word in a line is the content for this variable 
 # Variables that need to be specified in this file:
-# foutpath, resname, logname, filename, mapname, setpath, setname
+# foutpath, resname, logname, filename, mapname, setname
+# setnumber, setpath (These two are only needed under --all/-a)
 #################################################################
 
 foutpath    Results/snp_results/
@@ -19,8 +20,10 @@ filename    Data/filenamelist.txt
 mapname	    Data/example_bt_tag.map
 setname	    Data/example_bt_tag.set
 
-# Format of .set/.snps names: locipair1/2/.../.set/snp
+# setpath is used for real data, so that we only read the BOOST data once 
+# in order to calculate the set pairs inside one run of rrintcc
 setpath	    all_sets/
+setnumber	1
 
 # mapname    CUHK_HKDRGWA_6445CC_Clean_Ch1-22.map
 

rrintcc_BOOST.cpp

@@ -19,7 +19,9 @@ The contigency table collection part is modified from BOOSTx64.c (Can YANG, 2010
 
 */
 
-// Format: ./rrintcc_BOOST --config configNames.txt --silent --max-cov 10000
+// Format: ./rrintcc_BOOST --config configNames.txt --silent --max-cov 10000 --all
+// --all means will read all .set files in setpath (with format: locipair0.set, locipair1.set,...)
+// setnumber and setpath in config file will only be activated under --all (-a)
 
 #include "utility.h"
 
@@ -41,6 +43,7 @@ int main(int argc, char* argv[])
     bool show_message	 = true;
 	bool skip_symm 		 = false;
 	bool set_test 		 = true;
+	bool all_sets_flag 		 = false;
 
 	// Used for combined p value calculation
 	double myth_pgates 	 = 0.05;
@@ -70,7 +73,8 @@ int main(int argc, char* argv[])
     		max_cov_cnt = atoi(argv[i+1]);
     	}
 
-    	//if (strcmp(argv[i], "--set") == 0 || strcmp(argv[i], "-s") == 0) 
+    	if (strcmp(argv[i], "--all") == 0 || strcmp(argv[i], "-a") == 0)
+	    	all_sets_flag = true;
 
     }
 
@@ -92,7 +96,7 @@ int main(int argc, char* argv[])
 	int n, p, ncase, nctrl;;  // n: number of samples; p: number of varibles
 
 	RInside R(argc, argv);
-	R.parseEvalQ("library(mvtnorm); library(corpcor)");
+	R.parseEvalQ("library(mvtnorm)");
 
 	clock_t st, ed;
 
@@ -104,7 +108,8 @@ int main(int argc, char* argv[])
 		printf("start getting the file names...\n");
 	}
 	st = clock();
-	GetFileNames(configname, foutpath, resname, logname, filename, mapname, setpath, setname, show_message);
+	GetFileNames(configname, foutpath, resname, logname, filename, mapname, setpath, setname, numSets, show_message);
+
 	ed = clock();
 	if (show_message) 
 	{
@@ -170,23 +175,33 @@ int main(int argc, char* argv[])
 		printf("start calculating the region interactions...\n");
 	}
 //	time(&st);
+
+	if (all_sets_flag && isFileExist(resname.c_str()))
+		remove(resname.c_str());
+
+	if (!all_sets_flag)
+		numSets = 1;
+
 	for(int i = 0; i < numSets; i++)
 	{
+		string fout = foutpath;
+
 		st = clock();
-		if (show_message && i > 0 && i%1000 == 0)
+		if (show_message && i%100 == 0)
 		{
 			printf("%d sets have been analyzed\n", i);
 		}
 
-
-		//string setname;
-		//setname = setpath + "locipair" + to_string(i+1) + ".set";
-
-		string fout = foutpath;
-		fout.append("snp_pair_results");
-		fout.append(to_string(i+1));
-		fout.append(".txt");
-
+		if (all_sets_flag) 
+		{
+			setname = setpath + "locipair" + to_string(i) + ".set";
+			fout.append("snp_pair_results");
+			fout.append(to_string(i));
+			fout.append(".txt");
+		} else
+		{
+			fout.append("snp_pair_results.txt");
+		}
 
 		// load .set data: Write sA, sB, and skip_symm inside
 		sA.clear();
@@ -201,17 +216,17 @@ int main(int argc, char* argv[])
 		ofstream EPI;
 		EPI.open(resname.c_str(), ofstream::app);
 		EPI.precision(4);
-		EPI << setw(8)  << "Pair " << to_string(i+1) << " | " 
+		EPI << setw(8)  << "Pair " << to_string(i) << " | " 
 			<< setw(8)  << "pmin: " << " "
 			<< setw(15) << pmin << "\n";
 		EPI.flush();
 		EPI.close();
 
 		ed = clock();
 
-		if (show_message) 
+		/*if (show_message) 
 		{	printf("cputime for calculating the region interactions: %f seconds.\n", (double)(ed - st)/ CLOCKS_PER_SEC);
-		}
+		}*/
 	}	
 
 

utility.cpp

@@ -22,7 +22,13 @@ string char2str(char *f)
 	return s2.str();
 }
 
-void GetFileNames(string cfname, string &foutpath, string &resname, string &logname, string &filename, string &mapname, string &setpath, string &setname, bool show_message)
+bool isFileExist(const char *fileName)
+{
+    std::ifstream infile(fileName);
+    return infile.good();
+}
+
+void GetFileNames(string cfname, string &foutpath, string &resname, string &logname, string &filename, string &mapname, string &setpath, string &setname, int &numSets, bool show_message)
 {
 	// Should not use printLOG cuz logname is not yet ready
 	if (cfname.empty()) {
@@ -33,7 +39,7 @@ void GetFileNames(string cfname, string &foutpath, string &resname, string &logn
 
 	if (show_message)
 	{
-		printf("file for filename configuration: %s\n", cfname);
+		printf("file for filename configuration: %s\n", cfname.c_str());
 	}
 	//printLOG("file for filename configuration: " + char2str(cfname) + "\n");
 
@@ -73,6 +79,13 @@ void GetFileNames(string cfname, string &foutpath, string &resname, string &logn
 			if (id == "setname")
 				iss >> setname;
 
+			if (id == "setnumber")
+			{
+				string tmpnumber;
+				iss >> tmpnumber;
+				numSets = stoi(tmpnumber);
+			}
+
 		}
 	} else {
 		fprintf(stderr, "can't open file: %s\n", cfname);
@@ -793,10 +806,10 @@ double CalcRegionInter(RInside &R, string fout, vector<bool> &pheno, BYTE **geno
 
 	double pmin = R.parseEval("1-pmvnorm(lower=qnorm(minpv/2),upper=-qnorm(minpv/2),mean=rep(0, numpv),corr=cori)");
 	ed = clock();
-	if (show_message)
+	/*if (show_message)
 	{
 		printf("cputime for calling R fucntions pmvnorm: %f seconds.\n", (double)(ed - st)/ CLOCKS_PER_SEC);
-	}
+	}*/
 	return pmin;
 
 }

utility.h

@@ -49,7 +49,7 @@ string int2str(int n);
 
 string char2str(char *f);
 
-void GetFileNames(string cfname, string &foutpath, string &resname, string &logname, string &filename, string &mapname, string &setpath, string &setname, bool show_message);
+void GetFileNames(string cfname, string &foutpath, string &resname, string &logname, string &filename, string &mapname, string &setpath, string &setname, int &numSets, bool show_message);
 
 void GetSnpInfo(string filename, vector<int> &snpchr, vector<string> &snpname, bool show_message);
 
@@ -63,4 +63,5 @@ double CalcRegionInter(RInside &R, string fout, vector<bool> &pheno, BYTE **geno
 
 void LDContrastTest(vector<bool> &pheno, vector<double> &zlist, vector<double> &plist, vector<int> &cov_index, BYTE **geno, double **geno_bar, vector<int> &sA, vector<int> &sB, bool skip_symm, int p, int n, int ncase, int nctrl, bool show_message);
 
+bool isFileExist(const char *fileName);
 #endif