gds::Param Struct Reference

#include <GenomicDataStream_virtual.h>

Public Member Functions
	Param ()
	Param (const string &file, string regionString="", const string &samples="-", const double MAF=0, const double minVariance=0, const int &chunkSize=10000, const bool &missingToMean=true, const bool &permuteFeatureOrder=false, const int &rndSeed=12345)
void	setField (const string &field_)
void	setRegions (const string &regionString)
vector< string >	getRegions () const
void	setSamplesFile (const string &file)
void	print (ostream &out) const

Public Attributes
string	file
string	fileSamples = ""
string	field = ""
vector< string >	regions
string	samples
double	MAF
double	minVariance
int	chunkSize
bool	missingToMean
FileType	fileType

Detailed Description

Store parameters to pass to GenomicDataStream

Constructor & Destructor Documentation

Param() [1/2]

gds::Param::Param ( )

inline

Param() [2/2]

gds::Param::Param ( const string & file, string regionString = "", const string & samples = "-", const double MAF = 0, const double minVariance = 0, const int & chunkSize = 10000, const bool & missingToMean = true, const bool & permuteFeatureOrder = false, const int & rndSeed = 12345 )

inline

constructor

Parameters

file	.vcf, .vcf.gz or .bcf file with tabix index
regionString	target in the format "chr2:1-12345". Multiple regions can be separated by one of ,\n\t, for example "chr2:1-12345, chr3:1000-8000". Setting region to "" includes all variants
samples	string of comma separated sample IDs to extract: "ID1,ID2,ID3"
MAF	minor allele frequency filter applied to variants with max value <= 2
minVariance	minimum variance filter applied to variants with max value < 2
chunkSize	number of variants to return per chunk
missingToMean	if true, set missing values to the mean dosage value. if false, set to NaN
permuteFeatureOrder	default is false. If true permute regions in regionString to avoid linkage disequilibrium betweeen nearby regions
rndSeed	random seed for permutation

Note that field must be set separately for VCF/BCF: field: "GT" for genotype strings, "DS" for dosage, or another other field stored as an integer or float. "GT" is the only string type supported

Member Function Documentation

getRegions()

vector< string > gds::Param::getRegions ( ) const

inline

print()

void gds::Param::print ( ostream & out ) const

inline

setField()

void gds::Param::setField ( const string & field_ )

inline

setRegions()

void gds::Param::setRegions ( const string & regionString )

inline

setSamplesFile()

void gds::Param::setSamplesFile ( const string & file )

inline

Custom path to PSAM/FAM file

Member Data Documentation

chunkSize

int gds::Param::chunkSize

field

string gds::Param::field = ""

file

string gds::Param::file

fileSamples

string gds::Param::fileSamples = ""

fileType

FileType gds::Param::fileType

MAF

double gds::Param::MAF

minVariance

double gds::Param::minVariance

missingToMean

bool gds::Param::missingToMean

regions

vector<string> gds::Param::regions

samples

string gds::Param::samples

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

• inst/include/GenomicDataStream_virtual.h