Homec4science
Diffusion scATAC-seq (master) Browse

scATAC-seq/src/Clustering/ReadModelComputer.hpp
269172e8f4efmaster

Last Change
Raw File

ReadModelComputer.hpp
View Options

#ifndef READMODELCOMPUTER_HPP
#define READMODELCOMPUTER_HPP
#include <ModelComputer.hpp>
#include <Matrix2D.hpp>
#include <Matrix4D.hpp>
#include <ThreadPool.hpp>
/*!
* \brief The ReadModelComputer class provides the
* bases to compute the read density models, as computed
* by one of the expectation maximization algorithm for
* read density data, given a data matrix and a partitition.
* The data partition must be a probability matrix, as
* returned by one of the classes deriving EMBase.
* The data must be a 2D matrix of dimensions NxL
* containing the number of reads mapping at L
* different positions in N different regions.
* The models returned are the weighted aggregations
* of the signal in each region, assigned to each
* class.
* The format of the model matrix returned is :
* 1) the number of classes
* 2) the model length + 1. The 1st column
* contains the class probabilities. The signal
* starts at the 2nd column. The 1st column sums
* up to 1.0
*/
class ReadModelComputer : public ModelComputer
{
public:
/*!
* \brief Constructs an object to retrieve
* the read model given the data and their
* classification results.
* \param data the read density data.
* Its dimensions are :
* 1) the number of regions
* 2) the length of each region
* \param post_prob the data class assignment
* probabilities. Its dimensions are :
* 1) the 1st dimension of the data matrix
* 2) the number of classes
* 3) the number of shift states
* 4) the number of flip states
* \param bckg_class whether the last class of the
* classification (posterior probabilities) is a
* background class.
* \param n_threads the number of parallel threads
* to run the computations. 0 means no parallel
* computing, everything is run on the main thread.
*/
ReadModelComputer(Matrix2D<int>&& data,
const Matrix4D<double>& post_prob,
bool bckg_class,
size_t n_threads) ;
/*!
* \brief Destructor.
*/
virtual ~ReadModelComputer() override ;
protected:
/*!
* \brief the threads.
*/
ThreadPool* threads ;
} ;
#endif // READMODELCOMPUTER_HPP
c4science · Help