double GenotypeCounter::getHWE() const {
double hweP = 0.0;
if (nHomRef + nHet + nHomAlt == 0 ||
(nHet < 0 || nHomRef < 0 || nHomAlt < 0)) {
hweP = 0.0;
} else {
hweP = SNPHWE(nHet, nHomRef, nHomAlt);
}
return hweP;
}
void snp_summary_exhwe_Processor(unsigned int *gt, unsigned int nids, double *out) {
unsigned int i; //,j,idx;
//unsigned int nids = (*Nids);
//char str;
unsigned int count[3];
double meaids,p;
count[0]=count[1]=count[2]=0;
p = 0.;
for (i=0;i<9;i++) out[i] = 0.;
for (i=0;i<nids;i++)
if (gt[i]) {
count[gt[i]-1]++;
p+=(gt[i]-1);
}
meaids = 1.*(count[0]+count[1]+count[2]);
out[0] = meaids;
out[1] = meaids/nids;
if (meaids>0)
out[2] = p/(2.*meaids);
else
out[2] = 0.0;
out[3] = count[0];
out[4] = count[1];
out[5] = count[2];
if (meaids>0) {
double qmax, maf, pmax, loglik0, loglik1, chi2lrt, fmax;
out[6] = SNPHWE(count[1],count[0],count[2]);
pmax = out[2];
qmax = 1.-pmax;
maf = qmax; if (pmax<qmax) maf = pmax;
if (maf>1.e-16) {
fmax = (4.*count[0]*count[2] - 1.*count[1]*count[1])/((2.*count[0]+1.*count[1])*(2.*count[2]+1.*count[1]));
loglik0 = 0.;
if (count[0]) loglik0 += 2.*count[0]*log(qmax);
if (count[1]) loglik0 += 1.*count[1]*log(2.*qmax*pmax);
if (count[2]) loglik0 += 2.*count[2]*log(pmax);
loglik1 = 0.;
if (count[0]) loglik1 += 1.*count[0]*log(qmax*qmax+qmax*pmax*fmax);
if (count[1]) loglik1 += 1.*count[1]*log(2.*qmax*pmax*(1.-fmax));
if (count[2]) loglik1 += 1.*count[2]*log(pmax*pmax+qmax*pmax*fmax);
chi2lrt = 2*(loglik1-loglik0);
out[7] = fmax;
out[8] = chi2lrt;
} else {
out[7] = 0.;//maf;
out[8] = 0.;
}
} else {
out[6] = 1.0;
}
}
int main (int argc, char *argv[]) {
//HARDY WEINBERG EQUILIBRIUM QUALITY CONTROL
//Get the data
Datacube datacube;
datacube.loadData(argv[1]);
datacube.setVariablesMeaning(argv[6]);
int countsCol = datacube.values.at(0).size() - 1;//The column with the counts
//Set the threshold
float threshold;
threshold = atof(argv[2]);
//Set the target variables index if the test will only be applied on controls
bool onlyOnControls = false;
int targetVarIndex = countsCol - 1;
int CONTROL_VAL;
if(argv[3][0] == '1')
{
onlyOnControls = true;
CONTROL_VAL = getControlValue(&datacube,targetVarIndex);
}
bool keep[countsCol];
for(int i=0; i<datacube.values.at(0).size(); ++i)
{
//initialize the values of the vectors
keep[i] = true;
}
//initialize the counters
int minorHom=0, majorHom=0, h1count=0, h2count=0, heterozygous=0;
//Check which variables pass the HWE QC
double pValue;
for(int column=0;column<countsCol;column++)
{
//Only if the variable is a SNP
if(datacube.getVariableType(column).compare("SNP")==0)
{
h1count = 0;h2count = 0; heterozygous = 0;
for(int row=0;row<datacube.values.size();row++)
{
//chech if only controls should be used
if(!onlyOnControls || (onlyOnControls && datacube.values.at(row).at(targetVarIndex) == CONTROL_VAL))
{
switch(datacube.values.at(row).at(column))
{
//count the minor alleles
case HOMOZYGOUS_1:
h1count += datacube.values.at(row).at(countsCol);
break;
//count the heterozygous alleles
case HETEROZYGOUS:
heterozygous += datacube.values.at(row).at(countsCol);
break;
//count the major alleles
case HOMOZYGOUS_2:
h2count += datacube.values.at(row).at(countsCol);
}
}
}
//Set the minor and major alleles
if(h1count<h2count)
{
minorHom = h1count;
majorHom = h2count;
}
else
{
minorHom = h2count;
majorHom = h1count;
}
//If no alleles were counted (e.g. all missing, no controls)
if(h1count == 0 && h2count==0 && heterozygous==0)
{
keep[column] = false;
}
else
{
//calculate the HWE pValue
pValue = SNPHWE(heterozygous,minorHom,majorHom);
//Check if the SNP will be kept
if(pValue < threshold )
keep[column] = false;
}
}
}
//Remove the variables that did not pass the HWE QC
datacube.removeVariables(keep);
//output the data cube
datacube.writeToFile(argv[4]);
//Output the XML contents describing the algorithm
ofstream outpXML;
outpXML.open(argv[5]);
outpXML << "<log>" << endl;
outpXML << "<QualityControl algorithm_name=\"Hardy Weinberg Equilibrium Test\" algorithmParamsSetting=\"threshold=" << argv[2];
outpXML << " only_on_controls=" << argv[3] << "\"/>" << endl;
outpXML << "</log>";
outpXML.close();
}
