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Interface GeneticMap

All Known Implementing Classes:

PlinkGeneticMap, PositionMap

public interface GeneticMap

Interface GeneticMap represents a genetic map for one or more chromosomes.

Instances of class GeneticMap are immutable.

Method Summary

Modifier and Type	Method and Description
int	basePos(int chrom, double geneticPosition) Returns the base position corresponding to the specified genetic map position.
double	genPos(int chrom, int basePosition) Returns the genetic map position of the specified genome coordinate.
double	genPos(Marker marker) Returns the genetic map position of the specified marker.
default double[]	genPos(Markers markers) Returns the an array of length hapPairs.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
default float[]	pRecomb(Markers markers, int nHaps, float ne) Returns the an array of length hapPairs.nMarkers() whose whose j-th element for j > 0 is the probability of recombination between marker j - 1 and marker j, and whose initial element is 0.
java.lang.String	toString() Returns a string representation of this genetic map.

Method Detail

basePos

int basePos(int chrom,
            double geneticPosition)

Returns the base position corresponding to the specified genetic map position. If the genetic position is not a map position then the base position is estimated from the nearest genetic map positions using linear interpolation.

Parameters:

chrom - the chromosome index

geneticPosition - the genetic position on the chromosome

Returns:

the base position corresponding to the specified genetic map position

Throws:

java.lang.IllegalArgumentException - if the calculated base position exceeds Integer.MAX_VALUE

java.lang.IllegalArgumentException - if this genetic map has no map positions for the specified chromosome

java.lang.IndexOutOfBoundsException - if chrom < 0 || chrom >= ChromIds.instance().size()

genPos

double genPos(Marker marker)

Returns the genetic map position of the specified marker. The genetic map position is estimated using linear interpolation.

Parameters:

marker - a genetic marker

Returns:

the genetic map position of the specified marker

Throws:

java.lang.IllegalArgumentException - if this genetic map has no map positions for the specified chromosome

java.lang.NullPointerException - if marker == null

genPos

double genPos(int chrom,
              int basePosition)

Returns the genetic map position of the specified genome coordinate. The genetic map position is estimated using linear interpolation.

Parameters:

chrom - the chromosome index

basePosition - the base coordinate on the chromosome

Returns:

the genetic map position of the specified genome coordinate

Throws:

java.lang.IllegalArgumentException - if this genetic map has no map positions for the specified chromosome

java.lang.IndexOutOfBoundsException - if chrom < 0 || chrom >= ChromIds.instance().size()

toString

java.lang.String toString()

Returns a string representation of this genetic map. The exact details of the representation are unspecified and subject to change.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this genetic map

genPos

default double[] genPos(Markers markers)

Returns the an array of length hapPairs.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.

Parameters:

markers - the list of markers

Returns:

an array of genetic map positions

Throws:

java.lang.NullPointerException - if markers == null

pRecomb

default float[] pRecomb(Markers markers,
                        int nHaps,
                        float ne)

Returns the an array of length hapPairs.nMarkers() whose whose j-th element for j > 0 is the probability of recombination between marker j - 1 and marker j, and whose initial element is 0. Any inter-marker genetic distances less than 1e-7 cM are increased to 1e-7 cM.

Parameters:

markers - the list of markers

nHaps - the number of haplotypes in the sample

ne - the effective population size

Returns:

an array of inter-marker recombination probabilities

Throws:

java.lang.IllegalArgumentException - if nHaps < 1

java.lang.IllegalArgumentException - if ne < 1f

java.lang.NullPointerException - if markers == null