gds::GenomicRanges Class Reference

#include <GenomicRanges.h>

Public Member Functions
	GenomicRanges ()
	GenomicRanges (const vector< string > &chrom, const vector< size_t > &start, const vector< size_t > &end)
	GenomicRanges (const vector< string > &regions)
	GenomicRanges (const string &regionString)
vector< string >	get_chrom () const
vector< size_t >	get_start () const
vector< size_t >	get_end () const
const string	get_chrom (const int &i) const
const size_t	get_start (const int &i) const
const size_t	get_end (const int &i) const
const int	size () const
const bool	isWithin (const size_t &start, const size_t &end, const size_t &position) const
const bool	isWithin (const string &chr, const size_t &position) const
const vector< int >	getWithinIndeces (vector< string > chr, vector< size_t > position)

Detailed Description

Store genomic ranges of type chrom:start-end

Constructor & Destructor Documentation

GenomicRanges() [1/4]

gds::GenomicRanges::GenomicRanges ( )

inline

GenomicRanges() [2/4]

gds::GenomicRanges::GenomicRanges ( const vector< string > & chrom, const vector< size_t > & start, const vector< size_t > & end )

inline

Constructor from vectors of chrom, start, end

GenomicRanges() [3/4]

gds::GenomicRanges::GenomicRanges ( const vector< string > & regions )

inline

Constructor from string of chr:start-end

GenomicRanges() [4/4]

gds::GenomicRanges::GenomicRanges ( const string & regionString )

inline

Constructor from string of delimited chr:start-end,chr:start-end for delim "\t,\n"

Member Function Documentation

get_chrom() [1/2]

vector< string > gds::GenomicRanges::get_chrom ( ) const

inline

Accessors

get_chrom() [2/2]

const string gds::GenomicRanges::get_chrom ( const int & i ) const

inline

get_end() [1/2]

vector< size_t > gds::GenomicRanges::get_end ( ) const

inline

get_end() [2/2]

const size_t gds::GenomicRanges::get_end ( const int & i ) const

inline

get_start() [1/2]

vector< size_t > gds::GenomicRanges::get_start ( ) const

inline

get_start() [2/2]

const size_t gds::GenomicRanges::get_start ( const int & i ) const

inline

getWithinIndeces()

const vector< int > gds::GenomicRanges::getWithinIndeces ( vector< string > chr, vector< size_t > position )

inline

get indeces of entries in position that are found in Genomic ranges. Currently quadratic time

isWithin() [1/2]

const bool gds::GenomicRanges::isWithin ( const size_t & start, const size_t & end, const size_t & position ) const

inline

Evaluate if position is within [start,end] inclusive

isWithin() [2/2]

const bool gds::GenomicRanges::isWithin ( const string & chr, const size_t & position ) const

inline

size()

const int gds::GenomicRanges::size ( ) const

inline

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

• inst/include/GenomicRanges.h