1#ifndef GSDECON_BLOCKED_HPP
2#define GSDECON_BLOCKED_HPP
9#include "scran_pca/scran_pca.hpp"
10#include "sanisizer/sanisizer.hpp"
48template<
typename Value_,
typename Index_,
typename Block_,
typename Float_>
50 if (internal::check_edge_cases(matrix, options.
rank, output)) {
54 scran_pca::BlockedPcaOptions bopt;
55 bopt.number = options.
rank;
56 bopt.scale = options.
scale;
62 const auto res = scran_pca::blocked_pca(matrix, block, bopt);
65 static_assert(!Eigen::MatrixXd::IsRowMajor);
66 const auto nfeat = res.center.cols();
67 const auto nblocks = res.center.rows();
68 auto block_means = sanisizer::create<std::vector<Float_> >(nblocks);
70 for (
decltype(I(nfeat)) f = 0; f < nfeat; ++f) {
71 for (
decltype(I(nblocks)) b = 0; b < nblocks; ++b) {
72 block_means[b] += res.center.coeff(b, f);
75 for (
auto& b : block_means) {
79 const auto ncells = res.components.cols();
80 for (
decltype(I(ncells)) c = 0; c < ncells; ++c) {
81 output.
scores[c] = block_means[block[c]];
83 internal::process_output(res.rotation, res.components, options.
scale, res.scale, output);
103template<
typename Float_ =
double,
typename Value_,
typename Index_,
typename Block_>
107#ifdef SCRAN_QC_TEST_INIT
111 sanisizer::resize(output.
scores, matrix.
ncol()
112#ifdef SCRAN_QC_TEST_INIT
Options for the gsdecon algorithm.
Classes for storing the results.
virtual Index_ ncol() const=0
virtual Index_ nrow() const=0
Gene set scoring with gsdecon.
Definition blocked.hpp:21
void compute_blocked(const tatami::Matrix< Value_, Index_ > &matrix, const Block_ *const block, const Options &options, const Buffers< Float_ > &output)
Definition blocked.hpp:49
Buffers for the results of compute() and compute_blocked().
Definition Results.hpp:18
Float_ * scores
Definition Results.hpp:23
Float_ * weights
Definition Results.hpp:29
Options for compute() and compute_blocked().
Definition Options.hpp:17
bool realize_matrix
Definition Options.hpp:63
int rank
Definition Options.hpp:33
scran_blocks::WeightPolicy block_weight_policy
Definition Options.hpp:45
scran_blocks::VariableWeightParameters variable_block_weight_parameters
Definition Options.hpp:51
int num_threads
Definition Options.hpp:57
irlba::Options irlba_options
Definition Options.hpp:68
bool scale
Definition Options.hpp:40
Results of compute() and compute_blocked().
Definition Results.hpp:37
std::vector< Float_ > weights
Definition Results.hpp:49
std::vector< Float_ > scores
Definition Results.hpp:42