CNVCaller Class Reference

#include <cnv_caller.h>

Collaboration diagram for CNVCaller:

Public Member Functions
	CNVCaller (InputData &input_data)
CNVData	run ()
std::vector< double >	calculateLogRRatiosAtSNPS (std::vector< int > snp_positions)
double	calculateMeanChromosomeCoverage ()
	Calculate the mean chromosome coverage.
double	calculateWindowLogRRatio (double mean_chr_cov, int start_pos, int end_pos)
std::pair< std::vector< int >, std::vector< double > >	readSNPBAFs ()
std::vector< double >	getSNPPopulationFrequencies (std::vector< int > snp_locations)
void	saveToTSV (std::string filepath, std::vector< int > snp_locations, std::vector< double > bafs, std::vector< double > logr_ratios, std::vector< int > state_sequence)

Private Attributes
InputData *	input_data
double	chr_mean_coverage = 0

Constructor & Destructor Documentation

CNVCaller()

CNVCaller::CNVCaller

(

InputData &

input_data

)

Member Function Documentation

calculateLogRRatiosAtSNPS()

std::vector< double > CNVCaller::calculateLogRRatiosAtSNPS

(

std::vector< int >

snp_positions

)

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calculateMeanChromosomeCoverage()

double CNVCaller::calculateMeanChromosomeCoverage

(

)

Calculate the mean chromosome coverage.

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calculateWindowLogRRatio()

double CNVCaller::calculateWindowLogRRatio	(	double	mean_chr_cov,
		int	start_pos,
		int	end_pos
	)

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getSNPPopulationFrequencies()

std::vector< double > CNVCaller::getSNPPopulationFrequencies

(

std::vector< int >

snp_locations

)

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readSNPBAFs()

std::pair< std::vector< int >, std::vector< double > > CNVCaller::readSNPBAFs

(

)

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run()

CNVData CNVCaller::run

(

)

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saveToTSV()

void CNVCaller::saveToTSV	(	std::string	filepath,
		std::vector< int >	snp_locations,
		std::vector< double >	bafs,
		std::vector< double >	logr_ratios,
		std::vector< int >	state_sequence
	)

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Member Data Documentation

chr_mean_coverage

double CNVCaller::chr_mean_coverage = 0

private

input_data

InputData* CNVCaller::input_data

private

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The documentation for this class was generated from the following files:

• include/cnv_caller.h
• src/cnv_caller.cpp