1#ifndef SCRAN_SUGGEST_ADT_QC_FILTERS_H
2#define SCRAN_SUGGEST_ADT_QC_FILTERS_H
4#include "../utils/macros.hpp"
80 detected_num_mads = n;
102 detected_num_mads= n;
114 min_detected_drop= m;
158 template<
bool overwrite = true,
typename Float,
typename Integer,
typename Output>
161 throw std::runtime_error(
"should use filter_blocked() for multiple batches");
163 filter_<overwrite>(n, buffers, output, [](
size_t i) ->
size_t {
return 0; });
177 template<
typename Output = u
int8_t>
179 std::vector<Output> output(metrics.
detected.size());
201 template<
bool overwrite = true,
typename Block,
typename Float,
typename Integer,
typename Output>
204 filter_<overwrite>(n, buffers, output, [&](
size_t i) -> Block {
return block[i]; });
206 filter<overwrite>(n, buffers, output);
224 template<
typename Output = u
int8_t,
typename Block>
226 std::vector<Output> output(metrics.
detected.size());
232 template<
bool overwrite,
typename Float,
typename Integer,
typename Output,
typename Function>
236 for (
size_t i = 0; i < n; ++i) {
239 if (quality_control::is_less_than<double>(buffers.
detected[i],
detected[b])) {
245 for (
size_t s = 0; s < nsubsets; ++s) {
256 if constexpr(overwrite) {
275 template<
typename Float,
typename Integer>
277 return run_blocked(n,
static_cast<int*
>(NULL), buffers);
304 template<
typename Block,
typename Float,
typename Integer>
307 std::vector<double> workspace(n);
308 std::vector<int> starts;
317 auto detected_res = meddler.
run_blocked(n, block, starts, buffers.
detected, workspace.data());
323 auto detected_filt = filter.
run(std::move(detected_res));
325 output.
detected = std::move(detected_filt.lower);
338 for (
size_t s = 0; s < nsubsets; ++s) {
340 auto subset_filt = filter.
run(std::move(subset_res));
341 output.
subset_totals.push_back(std::move(subset_filt.upper));
359 template<
typename Block>
Define outlier filters using a MAD-based approach.
Compute per-cell quality control metrics from an ADT count matrix.
Create filters to identify low-quality cells from ADT-derived QC metrics.
Definition SuggestAdtQcFilters.hpp:50
Thresholds run_blocked(size_t n, const Block *block, const PerCellAdtQcMetrics::Buffers< Float, Integer > &buffers) const
Definition SuggestAdtQcFilters.hpp:305
SuggestAdtQcFilters & set_detected_num_mads(double n=Defaults::num_mads)
Definition SuggestAdtQcFilters.hpp:79
SuggestAdtQcFilters & set_subset_num_mads(double n=Defaults::num_mads)
Definition SuggestAdtQcFilters.hpp:90
Thresholds run(const PerCellAdtQcMetrics::Results &metrics) const
Definition SuggestAdtQcFilters.hpp:286
SuggestAdtQcFilters & set_num_mads(double n=Defaults::num_mads)
Definition SuggestAdtQcFilters.hpp:101
SuggestAdtQcFilters & set_min_detected_drop(double m=Defaults::min_detected_drop)
Definition SuggestAdtQcFilters.hpp:113
Thresholds run_blocked(const PerCellAdtQcMetrics::Results &metrics, const Block *block) const
Definition SuggestAdtQcFilters.hpp:360
Thresholds run(size_t n, const PerCellAdtQcMetrics::Buffers< Float, Integer > &buffers) const
Definition SuggestAdtQcFilters.hpp:276
Functions for single-cell RNA-seq analyses.
Definition AggregateAcrossCells.hpp:18
Define outlier filters from the median and MAD.
Definition ChooseOutlierFilters.hpp:30
ChooseOutlierFilters & set_min_diff(double m=Defaults::min_diff)
Definition ChooseOutlierFilters.hpp:104
ChooseOutlierFilters & set_num_mads(double n=Defaults::num_mads)
Definition ChooseOutlierFilters.hpp:92
ChooseOutlierFilters & set_lower(bool l=Defaults::lower)
Definition ChooseOutlierFilters.hpp:70
Thresholds run(ComputeMedianMad::Results x) const
Definition ChooseOutlierFilters.hpp:273
ChooseOutlierFilters & set_upper(bool u=Defaults::upper)
Definition ChooseOutlierFilters.hpp:81
Buffers for direct storage of the calculated statistics.
Definition PerCellAdtQcMetrics.hpp:69
Integer * detected
Definition PerCellAdtQcMetrics.hpp:78
std::vector< Float * > subset_totals
Definition PerCellAdtQcMetrics.hpp:84
Result store for QC metric calculations.
Definition PerCellAdtQcMetrics.hpp:125
std::vector< int > detected
Definition PerCellAdtQcMetrics.hpp:144
Buffers buffers()
Definition PerCellAdtQcMetrics.hpp:157
Default parameters.
Definition SuggestAdtQcFilters.hpp:55
static constexpr double min_detected_drop
Definition SuggestAdtQcFilters.hpp:64
static constexpr double num_mads
Definition SuggestAdtQcFilters.hpp:59
Thresholds to define outliers on each metric.
Definition SuggestAdtQcFilters.hpp:126
std::vector< double > detected
Definition SuggestAdtQcFilters.hpp:132
void filter(size_t n, const PerCellAdtQcMetrics::Buffers< Float, Integer > &buffers, Output *output) const
Definition SuggestAdtQcFilters.hpp:159
void filter_blocked(size_t n, const Block *block, const PerCellAdtQcMetrics::Buffers< Float, Integer > &buffers, Output *output) const
Definition SuggestAdtQcFilters.hpp:202
std::vector< std::vector< double > > subset_totals
Definition SuggestAdtQcFilters.hpp:139
std::vector< Output > filter(const PerCellAdtQcMetrics::Results &metrics) const
Definition SuggestAdtQcFilters.hpp:178
std::vector< Output > filter_blocked(const PerCellAdtQcMetrics::Results &metrics, const Block *block) const
Definition SuggestAdtQcFilters.hpp:225