void Data::bed2diffs_v1()
{
std::string diffsfile = datapath + ".diffs";
std::string countfile = datapath + ".count";
std::string orderfile = datapath + ".order";
std::ofstream outdiffs(diffsfile.c_str(), std::ios::out);
std::ofstream outcount(countfile.c_str(), std::ios::out);
std::ofstream outorder(orderfile.c_str(), std::ios::out);
outdiffs.precision(12);
outdiffs.setf(std::ios::fixed,std::ios::floatfield);
size_t nPairs = nIndiv*(nIndiv-1)/2;
size_t nSitesProcessed = 0;
// Read the genotypes in serial, compute the differences in parallel
snp_t *snps = (snp_t *) malloc( sizeof(snp_t)*nIndiv );
size_t *a = (size_t *) malloc( sizeof(size_t)*nPairs );
size_t *b = (size_t *) malloc( sizeof(size_t)*nPairs );
double *diffs = (double *) malloc( sizeof(double)*nPairs );
double *pairs = (double *) malloc( sizeof(double)*nPairs );
for (size_t i = 0 ; i<(nIndiv-1) ; i++ ) {
for (size_t j = i+1 ; j<nIndiv ; j++ ) {
size_t ij = Index(i,j);
diffs[ij] = 0.0;
pairs[ij] = 0.0;
a[ij] = i;
b[ij] = j;
}
}
while (pio_next_row( &plink_file, snps ) == PIO_OK) {
nSitesProcessed++;
#pragma omp parallel for
for (size_t ij = 0 ; ij < nPairs ; ij++ ) {
size_t zi = snps[a[ij]];
size_t zj = snps[b[ij]];
if ((zi!=PLINK_NA)&&(zj!=PLINK_NA)) {
diffs[ij] += (zi - zj)*(zi - zj);
pairs[ij] += 1.0;
}
}
}
std::cout << "Computed average pairwise differences across " << nSitesProcessed << " SNPs" << std::endl;
if (!outdiffs.is_open() || !outorder.is_open())
{
std::cerr << "[Data::bed2diffs] Error writing output files" << std::endl;
exit(1);
}
for (size_t i = 0 ; i<nIndiv ; i++ ) {
struct pio_sample_t *sample = pio_get_sample( &plink_file, i );
outorder << sample->fid << " " << sample->iid << std::endl;
for (size_t j = 0 ; j<nIndiv ; j++ ) {
if (i==j) {
outdiffs << " " << 0;
} else {
size_t ij = Index(i,j);
outdiffs << " " << diffs[ij]/pairs[ij];
outcount << " " << pairs[ij];
}
}
outdiffs << std::endl;
outcount << std::endl;
}
outdiffs.close( );
outcount.close( );
outorder.close( );
free( a );
free( b );
free( snps );
free( diffs );
free( pairs );
}
void Data::bed2diffs_v2()
{
std::string diffsfile = datapath + ".diffs";
std::string orderfile = datapath + ".order";
std::ofstream outdiffs(diffsfile.c_str(), std::ios::out);
std::ofstream outorder(orderfile.c_str(), std::ios::out);
outdiffs.precision(12);
outdiffs.setf(std::ios::fixed,std::ios::floatfield);
size_t nPairs = nIndiv*(nIndiv-1)/2;
size_t nSitesProcessed = 0;
// Read the genotypes in serial, compute the differences in parallel
snp_t *snps = (snp_t *) malloc( sizeof(snp_t)*nIndiv );
size_t *a = (size_t *) malloc( sizeof(size_t)*nPairs );
size_t *b = (size_t *) malloc( sizeof(size_t)*nPairs );
double *diffs = (double *) malloc( sizeof(double)*nPairs );
double *count = (double *) malloc( sizeof(double)*nPairs );
for (size_t i = 0 ; i < (nIndiv-1) ; i++ ) {
for (size_t j = i+1 ; j < nIndiv ; j++ ) {
size_t ij = Index(i, j);
diffs[ij] = 0.0;
count[ij] = 0.0;
a[ij] = i;
b[ij] = j;
}
}
while (pio_next_row( &plink_file, snps ) == PIO_OK) {
nSitesProcessed++;
// Compute the observed genotype mean
int sumGeno = 0, nObsrvd = 0;
for (size_t i = 0 ; i < nIndiv ; i++ ) {
size_t zi = snps[i];
if (zi != PLINK_NA) {
sumGeno += zi; nObsrvd += 1;
}
}
double aveGeno = sumGeno / (double)nObsrvd;
#pragma omp parallel for
for (size_t ij = 0 ; ij < nPairs ; ij++ ) {
// If a genotype missing, impute it with the average genotype (which is a double, not an int)
double zi = (double)snps[a[ij]];
double zj = (double)snps[b[ij]];
if (zi == PLINK_NA) { zi = aveGeno; }
if (zj == PLINK_NA) { zj = aveGeno; }
diffs[ij] += (zi - zj) * (zi - zj);
count[ij] += 1.0;
}
}
std::cout << "Computed average pairwise differences across " << nSitesProcessed << " SNPs" << std::endl;
if (!outdiffs.is_open() || !outorder.is_open())
{
std::cerr << "[Data::bed2diffs] Error writing output files" << std::endl;
exit(1);
}
for (size_t i = 0 ; i < nIndiv ; i++ ) {
struct pio_sample_t *sample = pio_get_sample( &plink_file, i );
outorder << sample->fid << " " << sample->iid << std::endl;
for (size_t j = 0 ; j < nIndiv ; j++ ) {
if (i == j) {
outdiffs << " " << 0;
} else {
size_t ij = Index(i, j);
outdiffs << " " << diffs[ij] / count[ij];
}
}
outdiffs << std::endl;
}
outdiffs.close( );
outorder.close( );
free( a );
free( b );
free( snps );
free( diffs );
free( count );
}
