cls.GlobalLDBlocks.CGlobalLDBlocks Class Reference

Global linkage disequilibrium (LD) blocks. More...

Public Member Functions
def	__init__ (s, paths)
	Constructor. More...
def	GetPaths (s)
	Get CPaths object stored here. More...
def	PosAndLD (s, chrom, pos)
	Is the position in an LD blocks? More...
def	SNPandGeneInLD (s, chrom, snpPos, gBegin, gEnd)
	Is the SNP/gene pair in LD? More...

Static Public Attributes
int	LD_ID_IDX = 0;
int	LD_BEGIN_IDX = 17;
int	LD_END_IDX = 18;
	ldBlocks = CGlobalLDBlocks(CPaths());

Detailed Description

Global linkage disequilibrium (LD) blocks.

Class for handling internal LD data. These data are characterized by
global blocks of LD, that is, by definition all nucleotides within such a
block are believed to be in LD. (Usually LD is computed for a pair of
points on a chromosome.) Blocks of LD were computed in-house.

Constructor & Destructor Documentation

__init__()

def cls.GlobalLDBlocks.CGlobalLDBlocks.__init__	(		s,
			paths
	)

Constructor.

Parameters

paths

CPaths object. False for 1000 Genomes LD block data.

Member Function Documentation

GetPaths()

def cls.GlobalLDBlocks.CGlobalLDBlocks.GetPaths

(

s

)

Get CPaths object stored here.

PosAndLD()

def cls.GlobalLDBlocks.CGlobalLDBlocks.PosAndLD	(		s,
			chrom,
			pos
	)

Is the position in an LD blocks?

Parameters

chrom	Chromosome number (String).
snpPos	SNP position on chromosome (Int).

Returns

Empty list, if not, otherwise a List of Tuples as returned by CStaticRTree.ClosestInterval.

SNPandGeneInLD()

def cls.GlobalLDBlocks.CGlobalLDBlocks.SNPandGeneInLD	(		s,
			chrom,
			snpPos,
			gBegin,
			gEnd
	)

Is the SNP/gene pair in LD?

    Specialized version for querying if a SNP and some associated gene are
    in LD, that is, are within the same LD block. Definition of 'within' a
    block of LD is: The SNP must be in an LD block and parts of the gene
    must also be covered by this block.

    @param chrom  Chromosome number (@c String).
    @param snpPos SNP position on chromosome (@c Int).
    @param gBegin Start position of gene on chromosome (@c Int).
    @param gEnd   End position of gene on chromosome (@c Int). gBegin >
     gEnd is ok and will be treated correctly.
    @return The LD block identifier. Returns @c None if the SNP/gene pair
     is not contained in any LD block.

Member Data Documentation

LD_BEGIN_IDX

int cls.GlobalLDBlocks.CGlobalLDBlocks.LD_BEGIN_IDX = 17;

static

LD_END_IDX

int cls.GlobalLDBlocks.CGlobalLDBlocks.LD_END_IDX = 18;

static

LD_ID_IDX

int cls.GlobalLDBlocks.CGlobalLDBlocks.LD_ID_IDX = 0;

static

ldBlocks

cls.GlobalLDBlocks.CGlobalLDBlocks.ldBlocks = CGlobalLDBlocks(CPaths());

static

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

• cls/GlobalLDBlocks.py