BayesicSpace::GenoTableBin Class Reference

Class to store binary compressed genotype tables. More...

#include <gvarHash.hpp>

Public Member Functions
	GenoTableBin ()
	Default constructor.
	GenoTableBin (const std::string &inputFileName, const uint32_t &nIndividuals, std::string logFileName)
	Constructor with input file name.
	GenoTableBin (const std::string &inputFileName, const uint32_t &nIndividuals, std::string logFileName, const size_t &nThreads)
	Constructor with input file name and thread count.
	GenoTableBin (const std::vector< int > &maCounts, const uint32_t &nIndividuals, std::string logFileName)
	Constructor with count vector.
	GenoTableBin (const std::vector< int > &maCounts, const uint32_t &nIndividuals, std::string logFileName, const size_t &nThreads)
	Constructor with count vector and thread count.
	GenoTableBin (const GenoTableBin &toCopy)=delete
	Copy constructor (deleted)
GenoTableBin &	operator= (const GenoTableBin &toCopy)=delete
	Copy assignment operator (deleted)
	GenoTableBin (GenoTableBin &&toMove) noexcept=default
	Move constructor.
GenoTableBin &	operator= (GenoTableBin &&toMove) noexcept=default
	Move assignment operator.
	~GenoTableBin ()=default
	Destructor.
void	saveGenoBinary (const std::string &outFileName) const
	Save the binary genotype file.
void	allJaccardLD (const InOutFileNames &bimAndLDnames, const size_t &suggestNchunks=static_cast< size_t >(1)) const
	All by all Jaccard similarity LD with locus names.
void	saveLogFile () const
	Save the log to a file.

Detailed Description

Class to store binary compressed genotype tables.

Converts genotype data to a lossy compressed binary code. Genotypes are stored in memory in a one-bit format: bit set for the minor allele, unset for the major. Bits corresponding to missing data are unset (this is the same as mean imputation), heterozygotes are set with a 50% probability.

Constructor & Destructor Documentation

GenoTableBin() [1/5]

BayesicSpace::GenoTableBin::GenoTableBin ( const std::string & inputFileName, const uint32_t & nIndividuals, std::string logFileName )

inline

Constructor with input file name.

The file should be in the plink .bed format. Heterozygotes are assigned the major or minor allele at random, missing genotypes are assigned the major allele. If necessary, alleles are re-coded so that the set bit is always the minor allele.

Parameters

[in]	inputFileName	input file name
[in]	nIndividuals	number of genotyped individuals
[in]	logFileName	name of the log file

GenoTableBin() [2/5]

BayesicSpace::GenoTableBin::GenoTableBin	(	const std::string &	inputFileName,
		const uint32_t &	nIndividuals,
		std::string	logFileName,
		const size_t &	nThreads )

Constructor with input file name and thread count.

The file should be in the plink .bed format. Heterozygotes are assigned the major or minor allele at random, missing genotypes are assigned the major allele. If necessary, alleles are re-coded so that the set bit is always the minor allele. The number of threads requested is maximum to be used, depending on available system resources.

Parameters

[in]	inputFileName	input file name
[in]	nIndividuals	number of genotyped individuals
[in]	logFileName	name of the log file
[in]	nThreads	maximal number of threads to use

GenoTableBin() [3/5]

BayesicSpace::GenoTableBin::GenoTableBin ( const std::vector< int > & maCounts, const uint32_t & nIndividuals, std::string logFileName )

inline

Constructor with count vector.

Input is a vector of minor allele counts (0, 1, or 2) or -9 for missing data. Heterozygotes are assigned the major or minor allele at random, missing genotypes are assigned the major allele. The counts are checked and re-coded if necessary so that set bits represent the minor allele. This function should run faster if the 0 is the major allele homozygote. While the above values are the norm, any negative number will be interpreted as missing, any odd number as 1, and any (non-0) even number as 2. The input is a vectorized matrix of genotypes. The original matrix has individuals on rows, and is vectorized by row.

Parameters

[in]	maCounts	vector of minor allele numbers
[in]	nIndividuals	number of genotyped individuals
[in]	logFileName	name of the log file

GenoTableBin() [4/5]

BayesicSpace::GenoTableBin::GenoTableBin	(	const std::vector< int > &	maCounts,
		const uint32_t &	nIndividuals,
		std::string	logFileName,
		const size_t &	nThreads )

Constructor with count vector and thread count.

Input is a vector of minor allele counts (0, 1, or 2) or -9 for missing data. Heterozygotes are assigned the major or minor allele at random, missing genotypes are assigned the major allele. The counts are checked and re-coded if necessary so that set bits represent the minor allele. This function should run faster if the 0 is the major allele homozygote. While the above values are the norm, any negative number will be interpreted as missing, any odd number as 1, and any (non-0) even number as 2. The input is a vectorized matrix of genotypes. The original matrix has individuals on rows, and is vectorized by row. The number of threads requested is maximum to be used, depending on available system resources.

Parameters

[in]	maCounts	vector of minor allele numbers
[in]	nIndividuals	number of genotyped individuals
[in]	logFileName	name of the log file
[in]	nThreads	maximal number of threads to use

GenoTableBin() [5/5]

BayesicSpace::GenoTableBin::GenoTableBin ( GenoTableBin && toMove )

defaultnoexcept

Move constructor.

Parameters

[in]

toMove

object to move

Member Function Documentation

allJaccardLD()

void BayesicSpace::GenoTableBin::allJaccardLD	(	const InOutFileNames &	bimAndLDnames,
		const size_t &	suggestNchunks = static_cast< size_t >(1) ) const

All by all Jaccard similarity LD with locus names.

Calculates linkage disequilibrium among all loci using Jaccard similarity and \(r^2\) as the statistics. Result is a vectorized lower triangle of the symmetric \(N \times N\) similarity matrix, where \(N\) is the number of loci. Row and column locus names are also included in the tab-delimited output file. The lower triangle is vectorized by column (i.e. all correlations of the first locus, then all remaining correlations of the second, etc.). If the result does not fit in RAM, calculates in blocks and saves to disk periodically.

Parameters

[in]	bimAndLDnames	name of the input .bim file that has locus names and the output LD value file name
[in]	suggestNchunks	force processing in chunks

operator=()

GenoTableBin & BayesicSpace::GenoTableBin::operator= ( GenoTableBin && toMove )

defaultnoexcept

Move assignment operator.

Parameters

[in]

toMove

object to be moved

Returns

GenoTableBin object

saveGenoBinary()

void BayesicSpace::GenoTableBin::saveGenoBinary

(

const std::string &

outFileName

)

const

Save the binary genotype file.

Saves the binary approximate genotype data to a binary file.

Parameters

[in]

outFileName

output file name

saveLogFile()

void BayesicSpace::GenoTableBin::saveLogFile

(

)

const

Save the log to a file.

Log file name provided at construction.

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

• gvarHash.hpp