Added test options and documentation; cleaned up code

Author: corbinq

Makefile

@@ -1,7 +1,7 @@
 VERSION=0.3
 
 CPPFLAGS= -Ofast -flto -pipe -I$(cdir)/src/htslib -I$(cdir)/src/cdflib -I$(cdir)/src/tabixpp -L$(cdir)/src/htslib -L$(cdir)/src/cdflib -L$(cdir)/src/tabixpp 
-CXXFLAGS= -std=c++11 -DNDEBUG 
+CXXFLAGS= -std=c++11 
 FFLAGS=
 LDFLAGS= -lz -lm
 

README.md

@@ -2,9 +2,8 @@
 
 A C++ tool for Gene-based Analysis with oMniBus, Integrative Tests
 
-- Implements SKAT, burden, and ACAT gene-based test methods using variant- or region-based functional annotations
-- Calculates annotation-stratified gene-based tests (e.g., TWAS/PrediXcan tests using eSNPs, gene-based tests using only coding variants, and gene-based tests using enhancer-to-target-gene maps)
-- Calculates omnibus gene-based tests by aggregating across annotation classes
+- Implements several gene-based test forms (quadratic: weighted sum of Zsq, linear: weighted sum of Z, and maximum Zsq) to aggregate GWAS single-variant summary statistics cross-referenced with variant- or region-based functional annotations
+- Calculates annotation-stratified gene-based tests (e.g., TWAS/PrediXcan tests using eSNPs, gene-based tests using only coding variants, and gene-based tests using enhancer-to-target-gene maps), and omnibus tests by combining p-values for each gene 
 - Inputs: GWAS association summary statistics file (chromosome, position, ref/alt allele, and z-score or beta-hat + se), annotation files, and LD reference panel
 
 
@@ -38,7 +37,7 @@ chr1  769200  769400  Enhancer  chr1:769200:769400  C1orf170:3.36|PERM1:3.36
 
 - Association tests for individual regulatory elements is reported in `*.stratified_out.txt` files, and gene-based p-values (aggregating across regulatory elements for each gene) in `*.summary_out.txt` files.
 
-- **Aggregation Methods for Regulatory Elements.** By default, GAMBIT aggregates test statistics across variants in regulatory elements using a weighted sum of single-variant chi-squared statistics (SKAT gene-based test).  To instead use weighted ACAT to combine single-variant p-values, specify `--acat`.
+- **Aggregation Methods for Regulatory Elements.** By default, GAMBIT aggregates test statistics across variants in regulatory elements using a weighted sum of single-variant chi-squared statistics (SKAT gene-based test).  To instead use weighted ACAT or HMP to combine single-variant p-values, specify `--no-skat` and a p-value combination method via `--pcomb`.
 
 #### Gene-Based Analysis with Coding and Other Annotated Variants 
 
@@ -57,7 +56,7 @@ UTR       UTR5              Utr5
 
 - **Gene-Based Test Output.** Test statistics stratified by gene and annotation subclass are provided in `*.stratified_out.txt` files, and gene-based p-values (aggregating across annotation classes for each gene) in `*.summary_out.txt` files.
 
-- **Variant Aggregation Methods.** By default, GAMBIT aggregates test statistics across variants using a weighted sum of single-variant chi-squared statistics (SKAT gene-based test).  To instead use weighted ACAT to combine single-variant p-values, specify `--acat`.
+- **Variant Aggregation Methods.** By default, GAMBIT aggregates test statistics across variants using a weighted sum of single-variant chi-squared statistics (SKAT gene-based test).  To instead use weighted ACAT or HMP to combine single-variant p-values, specify `--no-skat` and a p-value combination method via `--pcomb`.
 
 #### TWAS Analysis
 - To compute TWAS/PrediXcan gene-based tests using GAMBIT, specify an eWeight file via `--eweights my_eWeights.txt.gz`, formatted
@@ -73,11 +72,11 @@ UTR       UTR5              Utr5
 
 - The `BETAS` field format is `eGene_A=Weight_A1@Tissue_A1;Weight_A2@Tissue_A2|eGene_B=Weight_B1@Tissue_B1`, and labels for tissue IDs can be specified in the header. 
 - **Subsetting tissues.** To restrict analysis to a subset of tissues/cell-types, specify a comma-separated list of tissues following the `--tissues` flag. By default, GAMBIT includes all tissues/cell-types present in the eWeight file. 
-- **Tissue Aggregation for Omnibus tests.** GAMBIT reports both single-tissue TWAS/PrediXcan analysis results, and omnibus tests results aggregating across all specified tissues/cell-types for each eGene. Omnibus p-values for multi-tissue TWAS/PrediXcan analysis can be calculated in GAMBIT using either 1) the maximum single-tissue test statistic based on the joint distribution of single-tissue statistics, 2) the sum of squared single-tissue z-scores (analogous to SKAT), or 3) ACAT [default]. Omnibus test method for multi-tissue analysis can be specified via `--tissue-aggreg` (`ACAT`, `MinP`, `SKAT`, or `ALL`).
+- **Tissue Aggregation for Omnibus tests.** GAMBIT reports both single-tissue TWAS/PrediXcan analysis results, and omnibus tests results aggregating across all specified tissues/cell-types for each eGene. Omnibus p-values for multi-tissue TWAS/PrediXcan analysis can be calculated in GAMBIT using either 1) the maximum single-tissue test statistic based on the joint distribution of single-tissue statistics, 2) the sum of squared single-tissue z-scores (analogous to SKAT), or 3) PCOMB for ACAT or HMP [default]. Omnibus test method for multi-tissue analysis can be specified via `--tissue-aggreg` (`PCOMB`, `MinP`, `SKAT`, or `ALL`). P-value combination method can be specified via `--pcomb` (`ACAT` or `HMP`).
 - **Single-tissue and omnibus test output.** Gene-based tests and p-values for each eGene-tissue pair are reported in `*.stratified_out.txt` files, and omnibus p-values (aggregating across all tissues for each eGene) in `*.summary_out.txt` files.
 
 #### dTSS-Weighted Gene-Based Tests
-- To incorporate un-annotated regulatory variants in gene-based analysis, GAMBIT implements a dTSS (distance to Transcription Start Site) weighted gene-based test, which aggregates all single-variant p-values within a specified window from each gene's TSS using ACAT and assigns higher weight to variants nearer the TSS using an exponential decay function. 
+- To incorporate un-annotated regulatory variants in gene-based analysis, GAMBIT implements a dTSS (distance to Transcription Start Site) weighted gene-based test, which aggregates all single-variant p-values within a specified window from each gene's TSS using weighted ACAT or HMP and assigns higher weight to variants nearer the TSS using an exponential decay function. 
 - To compute dTSS-weighted gene-based tests, specify a TSS bed file via `--tss-bed my_tss_bed.bed.gz`, fomatted 
 
 ```

bin/GAMBIT

@@ -20,9 +20,10 @@ void print_usage() {
 	cerr << "      --ldref-only : only retain variants with complete LD information\n";
 	cerr << "      --tissues STR : only use eSNPs from tissues listed in file\n";
 	cerr << "    test statistics\n";
+	cerr << "      --pcomb : p-value combination method (\"ACAT\" or \"HMP\") \n";
 	cerr << "      --tss-alpha : alpha values (comma-separated) for dTSS weights \n";
-	cerr << "      --acat : use ACAT rather than SKAT for regulatory elements & exons\n";
-	cerr << "      --tissue-aggreg [ACAT] : method to aggregate eSNP tests across tissues (\"ACAT\", \"MinP\", \"SKAT\", or \"All\") \n";
+	cerr << "      --no-skat : use ACAT or HMP rather than SKAT for regulatory elements & exons\n";
+	cerr << "      --tissue-aggreg: method to aggregate eSNP tests across tissues (\"PCOMB\" for ACAT/HMP (default), \"MaxZsq\", \"SKAT\", or \"All\") \n";
 	cerr << "      --tissues STR : only use eSNPs from listed tissues (comma-separated list or file)\n";
 	cerr << "    output\n";
 	cerr << "      --region STR : restrict analysis to specified region \n";
@@ -74,7 +75,9 @@ int main (int argc, char *argv[]) {
 
 	char default_test = 'Q'; // default is 'Q' (SKAT)
 
-	int cauchy_no_skat = 0;
+	int pcomb_no_skat = 0;
+	
+	string PCOMB_METHOD = "HMP";
 
 	string TSS_VERBOSITY_PVAL_STR = "";
 	double TSS_VERBOSITY_PVAL = 1.00;
@@ -93,6 +96,7 @@ int main (int argc, char *argv[]) {
 		{"no-memo", no_argument, &no_memo_LD, 1},
 		{"preload", no_argument, &preload_LD, 1},
 		{"ldref",      required_argument,  0,  'l'},
+		{"pcomb",      required_argument,  0,  'z'},
 		{"gwas", required_argument, 0, 'g'},
 		{"anno-defs", required_argument, 0, 'a'},
 		{"defs", required_argument, 0, 'a'},
@@ -107,7 +111,7 @@ int main (int argc, char *argv[]) {
 		{"merge-tissues", no_argument, &tmerge, 1},
 		{"tissue-aggreg", required_argument, 0, 'm'},
 		{"debug", no_argument, &debug_mode, 1},
-		{"acat", no_argument, &cauchy_no_skat, 1},
+		{"no-skat", no_argument, &pcomb_no_skat, 1},
 		{"stdout", no_argument, &print_screen, 1},
 		{"bayes", no_argument, &bayes, 1},
 		{"region",    required_argument, 0,  'r' },
@@ -118,7 +122,7 @@ int main (int argc, char *argv[]) {
 		{0, 0, 0, 0}
 	};
 	int long_index =0;
-	while ((opt = getopt_long(argc,argv,"l:g:a:f:s:x:y:e:j:t:b:m:r:p:v:",long_options,&long_index)) != -1) {
+	while ((opt = getopt_long(argc,argv,"l:g:a:f:s:x:y:z:e:j:t:b:m:r:p:v:",long_options,&long_index)) != -1) {
 		switch (opt) {
 			case 'f' : afile = optarg;
 				break;
@@ -142,6 +146,8 @@ int main (int argc, char *argv[]) {
 				break;
 			case 'y' : TSS_WINDOW_STR = optarg;
 				break;
+			case 'z' : PCOMB_METHOD = optarg;
+				break;
 			case 'e' : TSS_VERBOSITY_PVAL_STR = optarg;
 				break;
 			case 'b' : bfile = optarg;
@@ -226,6 +232,8 @@ int main (int argc, char *argv[]) {
 		setPreload(false);
 	}
 
+	setCombPvalMethod(PCOMB_METHOD);
+	
 	setMultiForm(multi_test_type);
 
 	if( JUMP_DIST_STR != "" ){
@@ -244,8 +252,8 @@ int main (int argc, char *argv[]) {
 
 	initCHR();
 
-	if( cauchy_no_skat ){
-		default_test = 'C'; // rather than SKAT, using Cauchy/ACAT test (no LD)
+	if( pcomb_no_skat ){
+		default_test = 'C'; // rather than SKAT, using ACAT/HMP test (no LD)
 	}
 
 	if( TSS_VERBOSITY_PVAL_STR != "" ){

src/Main.cpp

@@ -0,0 +1,32 @@
+#include "distributionFunctions.hpp"
+
+using namespace std;
+
+double pchisq( double stat, double df) {
+	double cdf, ccdf;
+	cumchi ( &stat, &df, &cdf, &ccdf );
+	return ccdf;
+}
+
+double pchisq( double stat, double df, double ncp) {
+	double cdf, ccdf;
+	cumchn( &stat, &df, &ncp, &cdf, &ccdf);
+	return ccdf;
+}
+
+double qchisq( double cdf, double df) {
+	double stat, ccdf, bd;
+	int which = 2;
+	ccdf = 1 - cdf;
+	int status;
+	cdfchi ( &which, &cdf, &ccdf, &stat, &df, &status, &bd );
+	return stat;
+}
+
+double pcauchy(double x){
+	return 0.5 + atan( x )/M_PI;
+}
+
+double qcauchy(double q){
+	return tan( M_PI*(q - 0.5) );
+}

src/distributionFunctions.cpp

@@ -0,0 +1,31 @@
+#ifndef DISTRIBUTIONFUNCTIONS_HPP
+#define DISTRIBUTIONFUNCTIONS_HPP
+
+#include "cdflib/cdflib.hpp"
+#include "eigenmvn/eigenmvn.hpp"
+#include "ROOT_Math/Landau.hpp"
+
+#include <iostream>
+#include <sstream>
+#include <fstream>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string>
+#include <algorithm>
+#include <vector>
+#include <unordered_map>
+#include <unordered_set>
+#include <set>
+#include <map>
+
+using namespace std;
+
+double pcauchy(double);
+double qcauchy(double);
+
+double pchisq(double, double);
+double pchisq(double, double, double);
+double qchisq(double, double);
+
+#endif