diff --git a/src/paramEst.cpp b/src/paramEst.cpp index 786a2ec..6b2cd07 100644 --- a/src/paramEst.cpp +++ b/src/paramEst.cpp @@ -358,7 +358,8 @@ arma::vec estHasemanElstonConstrained(const arma::mat& Z, const arma::mat& PREML arma::vec _he_update(c+1); // use RcppML NNLS (needs casting Eigen <-> arma) - _he_update = solveQP(vecZ, Ybig, _he_update); + // _he_update = solveQP(vecZ, Ybig, _he_update); + _he_update = nnlsSolve(vecZ, Ybig, _he_update, Iters); return _he_update; } @@ -388,7 +389,8 @@ arma::vec estHasemanElstonConstrainedML(const arma::mat& Z, const Rcpp::List& u_ // solve by linear least squares arma::vec _he_update(c+1); - _he_update = solveQP(vecZ, Ybig, _he_update); + // _he_update = solveQP(vecZ, Ybig, _he_update); + _he_update = nnlsSolve(vecZ, Ybig, _he_update, Iters); return _he_update; } @@ -421,7 +423,8 @@ arma::vec estHasemanElstonConstrainedGenetic(const arma::mat& Z, const arma::mat arma::mat vecZ = vectoriseZGenetic(Z, u_indices, PREML, PZ, Kin); // projection already applied arma::vec _he_update(c+1); - _he_update = solveQP(vecZ, Ybig, _he_update); + // _he_update = solveQP(vecZ, Ybig, _he_update); + _he_update = nnlsSolve(vecZ, Ybig, _he_update, Iters); return _he_update; } @@ -451,7 +454,8 @@ arma::vec estHasemanElstonConstrainedGeneticML(const arma::mat& Z, arma::mat vecZ = vectoriseZGeneticML(Z, u_indices, Kin); // projection already applied arma::vec _he_update(c+1); - _he_update = solveQP(vecZ, Ybig, _he_update); + // _he_update = solveQP(vecZ, Ybig, _he_update); + _he_update = nnlsSolve(vecZ, Ybig, _he_update, Iters); return _he_update; } diff --git a/vignettes/milo_glmm.Rmd b/vignettes/milo_glmm.Rmd index 9fabd6a..c6d31d7 100644 --- a/vignettes/milo_glmm.Rmd +++ b/vignettes/milo_glmm.Rmd @@ -167,7 +167,7 @@ set.seed(42) rownames(pbmc.design) <- pbmc.design$ObsID da_results <- testNhoods(pbmc.milo, design = ~ adjmfc.time + (1|tenx_lane), design.df = pbmc.design, fdr.weighting="graph-overlap", - glmm.solver="Fisher", REML=TRUE, norm.method="TMM", BPPARAM = bpparam, fail.on.error=FALSE, intercept.type="fixed") + glmm.solver="Fisher", REML=TRUE, norm.method="TMM", BPPARAM = bpparam, fail.on.error=FALSE) table(da_results$SpatialFDR < 0.1) ```