// Reconstruct block in the image sequence after thresholding
arma::cube Reconstruct(double lambda) {
arma::cube v = arma::zeros<arma::cube>(Nx, Ny, T);
arma::cube weights = arma::zeros<arma::cube>(Nx, Ny, T);
arma::mat block, Ublock, Vblock;
arma::vec Sblock;
block.set_size(Bs*Bs, T);
Ublock.set_size(Bs*Bs, T);
Sblock.set_size(T);
Vblock.set_size(T, T);
#pragma omp parallel for shared(v, weights) \
private(block, Ublock, Sblock, Vblock)
for (int it = 0; it < newVecSize; it++) {
Ublock = U[it];
Sblock = S[it];
Vblock = V[it];
// Basic singular value thresholding
// arma::vec Snew = arma::sign(Sblock)
// % arma::max(
// arma::abs(Sblock) - lambda,
// arma::zeros<arma::vec>(T));
// Gaussian-weighted singular value thresholding
arma::vec wvec = arma::abs(Sblock.max()
* arma::exp(-1
* lambda
* arma::square(Sblock)/2));
// Apply threshold
arma::vec Snew = arma::sign(Sblock)
% arma::max(
arma::abs(Sblock) - wvec,
arma::zeros<arma::vec>(T));
// Reconstruct from SVD
block = Ublock * diagmat(Snew) * Vblock.t();
// Deal with block weights (TODO: currently all weights = 1)
for (int k = 0; k < T; k++) {
int newy = patches(0, actualpatches(it), k);
int newx = patches(1, actualpatches(it), k);
v(arma::span(newy, newy+Bs-1),
arma::span(newx, newx+Bs-1),
arma::span(k, k)) += arma::reshape(block.col(k), Bs, Bs);
weights(arma::span(newy, newy+Bs-1),
arma::span(newx, newx+Bs-1),
arma::span(k, k)) += arma::ones<arma::mat>(Bs, Bs);
}
}
// Include the weighting
v /= weights;
v.elem(find_nonfinite(v)).zeros();
return v;
}
// [[Rcpp::export]]
arma::mat BeQTL2(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tC = cor(A.rows(Bootmat.row(i)),B.rows(Bootmat.row(i)));
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
inline
uvec
find_nonfinite(const BaseCube<typename T1::elem_type,T1>& X)
{
arma_extra_debug_sigprint();
typedef typename T1::elem_type eT;
const unwrap_cube<T1> tmp(X.get_ref());
const Mat<eT> R( const_cast< eT* >(tmp.M.memptr()), tmp.M.n_elem, 1, false );
return find_nonfinite(R);
}
//Script that takes two matrices, performs bootstrapped correlation, and returns the median
// [[Rcpp::export]]
arma::mat BeQTL(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
Rcpp::Rcout<<"Starting Bootstrap!"<<std::endl;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tA(A.n_rows,A.n_cols);
arma::mat tB(B.n_rows,B.n_cols);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tA = A.rows(Bootmat.row(i));
tB = B.rows(Bootmat.row(i));
tC = cor(tA,tB);
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
//Function to perform point estimate of correlation
// [[Rcpp::export]]
arma::mat PointCor(const arma::mat & A, const arma::mat & B){
arma::mat C= cor(A,B);
C.elem(find_nonfinite(C)).zeros();
return C;
}
