regdata::regdata(phedata &phed, gendata &gend, const int snpnum,
const bool ext_is_interaction_excluded)
{
freq = 0;
gcount = 0;
nids = gend.nids;
masked_data = new unsigned short int[nids];
for (int i = 0; i < nids; i++)
{
masked_data[i] = 0;
}
ngpreds = gend.ngpreds;
if (snpnum >= 0)
{
ncov = phed.ncov + ngpreds;
}
else
{
ncov = phed.ncov;
}
noutcomes = phed.noutcomes;
X.reinit(nids, (ncov + 1));
Y.reinit(nids, noutcomes);
for (int i = 0; i < nids; i++)
{
X.put(1., i, 0);
Y.put((phed.Y).get(i, 0), i, 0);
}
for (int j = 1; j <= phed.ncov; j++)
{
for (int i = 0; i < nids; i++)
{
X.put((phed.X).get(i, j - 1), i, j);
}
}
if (snpnum > 0)
for (int j = 0; j < ngpreds; j++)
{
double *snpdata = new double[nids];
gend.get_var(snpnum * ngpreds + j, snpdata);
for (int i = 0; i < nids; i++)
{
X.put(snpdata[i], i, (ncov - ngpreds + 1 + j));
}
delete[] snpdata;
}
// for (int i=0;i<nids;i++)
// for (int j=0;j<ngpreds;j++)
// X.put((gend.G).get(i,(snpnum*ngpreds+j)),i,(ncov-ngpreds+1+j));
is_interaction_excluded = ext_is_interaction_excluded;
}
/**
* Constructor that fills a regdata object with phenotype and genotype
* data.
*
* \param phed Reference to a phedata object with phenotype data
* \param gend Reference to a gendata object with genotype data
* \param snpnum The number of the SNP in the genotype data object to
* be added to the design matrix regdata::X. When set to a number < 0
* no SNP data is added to the design matrix (e.g. when calculating
* the null model).
*/
regdata::regdata(const phedata &phed,
const gendata &gend,
const int snpnum)
{
freq = 0;
gcount = 0;
nids = gend.nids;
masked_data = std::vector<bool>(nids, false);
ngpreds = gend.ngpreds;
if (snpnum >= 0)
{
ncov = phed.ncov + ngpreds;
}
else
{
ncov = phed.ncov;
}
noutcomes = phed.noutcomes;
X.reinit(nids, (ncov + 1));
Y.reinit(nids, noutcomes);
for (int i = 0; i < nids; i++)
{
X.put(1., i, 0);
Y.put((phed.Y).get(i, 0), i, 0);
}
for (int j = 1; j <= phed.ncov; j++)
{
for (int i = 0; i < nids; i++)
{
X.put((phed.X).get(i, j - 1), i, j);
}
}
if (snpnum > 0)
for (int j = 0; j < ngpreds; j++)
{
double *snpdata = new double[nids];
gend.get_var(snpnum * ngpreds + j, snpdata);
for (int i = 0; i < nids; i++)
{
X.put(snpdata[i], i, (ncov - ngpreds + 1 + j));
}
delete[] snpdata;
}
// for (int i=0;i<nids;i++)
// for (int j=0;j<ngpreds;j++)
// X.put((gend.G).get(i,(snpnum*ngpreds+j)),i,(ncov-ngpreds+1+j));
}
/**
* Constructor that fills a coxph_data object with phenotype and genotype
* data.
*
* @param phed Reference to a phedata object with phenotype data
* @param gend Reference to a gendata object with genotype data
* @param snpnum The number of the SNP in the genotype data object to
* be added to the design matrix regdata::X. When set to a number < 0
* no SNP data is added to the design matrix (e.g. when calculating
* the null model).
*/
coxph_data::coxph_data(const phedata &phed, const gendata &gend,
const int snpnum)
{
freq = 0;
gcount = 0;
nids = gend.nids;
masked_data = std::vector<bool>(nids, false);
ngpreds = gend.ngpreds;
if (snpnum >= 0)
{
ncov = phed.ncov + ngpreds;
}
else
{
ncov = phed.ncov;
}
if (phed.noutcomes != 2)
{
std::cerr << "coxph_data: number of outcomes should be 2 (now: "
<< phed.noutcomes << ")\n";
exit(1);
}
X.reinit(nids, (ncov + 1)); // Note: ncov takes ngpreds into
// account, see above!
stime.reinit(nids, 1);
sstat.reinit(nids, 1);
weights.reinit(nids, 1);
offset.reinit(nids, 1);
strata.reinit(nids, 1);
order.reinit(nids, 1);
for (int i = 0; i < nids; i++)
{
stime[i] = (phed.Y).get(i, 0);
sstat[i] = static_cast<int>((phed.Y).get(i, 1));
if (sstat[i] != 1 && sstat[i] != 0)
{
std::cerr << "coxph_data: status not 0/1 "
<<"(correct order: id, fuptime, status ...)"
<< endl;
exit(1);
}
}
// Add a column with a constant (=1) to the X matrix (the mean)
for (int i = 0; i < nids; i++)
{
X.put(1., i, 0);
}
// Insert the covariate data into X (note we use phed.ncov and not
// ncov, which includes ngpreds is not computing the null model!)
for (int j = 1; j <= phed.ncov; j++)
{
for (int i = 0; i < nids; i++)
{
X.put((phed.X).get(i, j - 1), i, j);
}
}
// Insert the genotype data into X
if (snpnum > 0)
{
for (int j = 0; j < ngpreds; j++)
{
double *snpdata = new double[nids];
gend.get_var(snpnum * ngpreds + j, snpdata);
for (int i = 0; i < nids; i++)
{
X.put(snpdata[i], i, (ncov - ngpreds + j));
}
delete[] snpdata;
}
}
for (int i = 0; i < nids; i++)
{
weights[i] = 1.0;
offset[i] = 0.0;
strata[i] = 0;
}
// sort by time
double *tmptime = new double[nids];
int *passed_sorted = new int[nids];
std::fill(passed_sorted, passed_sorted + nids, 0);
for (int i = 0; i < nids; i++)
{
tmptime[i] = stime[i];
}
qsort(tmptime, nids, sizeof(double), cmpfun);
for (int i = 0; i < nids; i++)
{
int passed = 0;
for (int j = 0; j < nids; j++)
{
if (tmptime[j] == stime[i])
{
if (!passed_sorted[j])
{
order[i] = j;
passed_sorted[j] = 1;
passed = 1;
break;
}
}
}
if (passed != 1)
{
std::cerr << "cannot recover element " << i << "\n";
exit(1);
}
}
stime = reorder(stime, order);
sstat = reorder(sstat, order);
weights = reorder(weights, order);
strata = reorder(strata, order);
offset = reorder(offset, order);
X = reorder(X, order);
// The coxfit2() function expects data in column major order.
X = transpose(X);
// X.print();
// offset.print();
// weights.print();
// stime.print();
// sstat.print();
delete[] tmptime;
delete[] passed_sorted;
}
