void xcount (int * m, int * k, double * count, int * safeSecs) {
countLimit = *count;
if (*count < 1) countLimit = 1e100; // Set limit to a huge number unless user asked for a limit
tableCount = 0;
// If there are only 2 alleles, that's a special case.
if (*k==2) {
*count = twoAlleleSpecialCase(m);
return;
}
// Set up global variables used during recursion
nAlleles = *k;
Rbytes = *k * sizeof(COUNTTYPE);
Rarray = Calloc(*k * *k * (*k-1)/2, COUNTTYPE);
for (int i = 0; i < nAlleles; i++) {
Rarray[i] = m[i];
}
hashCoefs = Calloc(nAlleles, unsigned long long);
hashCoefs[0] = m[0] + 1;
for (int i = 1; i < nAlleles; i++) {
hashCoefs[i] = hashCoefs[i-1] * (m[i] + 1);
}
nextNode = 0;
timeLimit = *safeSecs;
start = time(NULL);
// ***************** This is the call to do all the work!
homozygote(nAlleles, Rarray);
//
*count = tableCount;
Free(hashCoefs);
Free(Rarray);
}
void xtest (int * rm,
int * rk,
double * robservedVals, // observed stats: LLR, Prob, U, X2
double * rPvals, // computed P values: LLR, Prob, U, X2
int * rstatID, // which statistic to use for histogram (1-4)
int * rhistobins, // number of bins for histogram. (no histogram if 0)
double * rhistobounds, // Two values indicating the range for histogram
double * rhistoData, // histogram data. length = histobounds.
int * rsafeSecs, // abort calculation after this many seconds
double * tables // the number of tables examined
)
{
// Set up global variables used during recursion
nAlleles = *rk;
pU = pLLR = pPr = pX2 =probSum = 0;
hProb = rhistoData;
Rbytes = *rk * sizeof(COUNTTYPE);
statID = *rstatID;
timeLimit = *rsafeSecs;
HN = *rhistobins;
start = time(NULL);
Rarray = Calloc(*rk * *rk * (*rk-1)/2, COUNTTYPE);
for (int i = 0; i < nAlleles; i++) Rarray[i] = rm[i];
mi = rm-1; // 1-based list of allele counts
tableCount = 0;
umean = 0; uvariance = 0;
// Make lookup tables
xlnx = Calloc(rm[0] + 1, double);
lnFact = Calloc(rm[0] + 1, double);
uTerm1 = Calloc(rm[0]/2 + 1, double);
uTerm2 = Calloc(rm[1]/2 + 1, double);
int biggesta11 = rm[0]/2;
int biggesta22 = rm[1]/2;
int biggesta21 = rm[1];
x211 = Calloc((biggesta11+1), double);
x222 = Calloc((biggesta22 + 1), double);
x221 = Calloc((biggesta21+1), double);
xlnx[0] = 0;
lnFact[0] = 0;
double lni;
for (int i = 1; i <= rm[0]; i++) {
lni = log(i);
xlnx[i] = lni * i;
lnFact[i] = lnFact[i-1] + lni;
}
for(int i = 0; i <= rm[0]/2; i++) uTerm1[i] = (double)i/rm[0];
for(int i = 0; i <= rm[1]/2; i++) uTerm2[i] = (double)i/rm[1];
size_t nsq = fmax(2, nAlleles * nAlleles);
exa = Calloc(nsq, double); // Expected numbers. Array uses extra space but saves time
int nGenes = 0;
for(int i = 0; i < nAlleles; i++) nGenes += rm[i];
ntotal = nGenes/2;
for(int i = 0; i < nAlleles; i++) {
exa[i * nAlleles + i] = (double)(rm[i] * rm[i])/(2.0 * nGenes);
for (int j = 0; j < i; j++) {
exa[i * nAlleles + j] = (double)(rm[i] * rm[j])/nGenes;
}
}
for(int i = 0; i <= biggesta11; i++) x211[i] = R_pow_di(exa[0] - i, 2)/exa[0];
for(int i = 0; i <= biggesta21; i++) x221[i] = R_pow_di(exa[nAlleles] - i, 2)/exa[nAlleles];
for(int i = 0; i <= biggesta22; i++) x222[i] = R_pow_di(exa[nAlleles + 1] - i, 2)/exa[nAlleles + 1];
// Get constant terms for LLR and Prob
constProbTerm = constLLRterm = 0;
for (int i = 0; i < nAlleles; i++) {
constProbTerm += lgammafn(rm[i] + 1); //lnFact[rm[i]];
constLLRterm += xlnx[rm[i]];
}
constProbTerm += log(2)*ntotal + lgammafn(ntotal+1) - lgammafn(nGenes +1);
constLLRterm += -log(2)*ntotal - log(ntotal) * ntotal;
// Get cutoffs for the four test statistics
double oneMinus = 0.9999999; // Guards against floating-point-equality-test errors
if(robservedVals[0] > 0.000000000001) robservedVals[0] = 0; // positive values are rounding errors
maxLLR = robservedVals[0] * oneMinus;
maxlPr = log(robservedVals[1]) * oneMinus;
minmaxU = robservedVals[2] * oneMinus;
minX2 = robservedVals[3] * oneMinus;
// Set up histogram
if (HN) {
switch (*rstatID) {
case 0: // LLR -- histobounds gives bounds for -2LLR
leftStat = rhistobounds[0]/(-2.0);
statSpan = -2.0 * HN/(rhistobounds[1] - rhistobounds[0]);
break;
case 1: // Prob -- histobounds gives bounds for -2ln(pr)
leftStat = rhistobounds[0]/(-2.0);
statSpan = -2.0 * HN/(rhistobounds[1] - rhistobounds[0]);
break;
case 2: // U score -- histobounds is actual bounds
leftStat = rhistobounds[0];
statSpan = (double)HN/(rhistobounds[1] - rhistobounds[0]);
break;
case 3: // X2 -- histobounds is actual bounds
leftStat = rhistobounds[0];
statSpan = (double)HN/(rhistobounds[1] - rhistobounds[0]);
break;
default:
break;
}
hProb = rhistoData;
for(int i = 0; i < HN; i++) hProb[i] = 0;
}
start = time(NULL);
if (nAlleles == 2) {
twoAlleleSpecialCase();
} else {
homozygote(nAlleles, 0, 0, 0, 0, Rarray);
}
*tables = tableCount;
rPvals[0] = pLLR;
rPvals[1] = pPr;
rPvals[2] = pU;
rPvals[3] = pX2;
if (tableCount < 0) for(int i = 0; i < 4; i++) rPvals[i] = -1; // Process timed out and p values are meaningless
// printf("\nU mean = %.8f", umean);
// printf("\nU variance = %.8f\n", uvariance - umean * umean);
Free(xlnx);Free(lnFact);Free(Rarray);
Free(exa); Free(uTerm1); Free(uTerm2);
Free(x211); Free(x221); Free(x222);
}