Package vcf

Interface GeneticMap

All Known Implementing Classes:

MarkerMap, PlinkGenMap, 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	Description
int	basePos(int chrom, double geneticPosition)	Returns the base position corresponding to the specified genetic map position.
static GeneticMap	geneticMap(java.io.File file, ChromInterval chromInt)	Constructs and returns a genetic map from the specified data.
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, double intensity)	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.
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

geneticMap

static GeneticMap geneticMap(java.io.File file,
                             ChromInterval chromInt)

Constructs and returns a genetic map from the specified data. If the specified map file is null, the returned genetic map will convert genome coordinates to genetic units by dividing by 1,000,000. If (chromInt != null) the genetic map will be restricted to chromosome chromInt.chrom().

Parameters:

file - a PLINK-format genetic map file with cM units

chromInt - a chromosome interval

Returns:

a genetic map from the specified data.

Throws:

java.lang.IllegalArgumentException - if any map position is infinite or NaN

java.lang.NumberFormatException - if the base position on any line of the map file is not a parsable integer

java.lang.NumberFormatException - if the genetic map position on any line of the map file is not a parsable double

java.lang.IllegalArgumentException - if a non-empty line of the specified genetic map file does not contain 4 fields

java.lang.IllegalArgumentException - if the map positions on each chromosome are not sorted in ascending order

java.lang.IllegalArgumentException - if there are duplicate base positions on a chromosome

java.lang.IllegalArgumentException - if all base positions on a chromosome have the same genetic map position

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.IllegalArgumentException - if this genetic map does not contain a map position for any specified marker

java.lang.NullPointerException - if markers == null

pRecomb

default float[] pRecomb(Markers markers,
                        double intensity)

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. The initial marker on a chromosome has recombination probability 0. Any inter-marker genetic distances less than 1e-7 cM are increased to 1e-7 cM.

Parameters:

markers - the list of markers

intensity - the reciprocal of the expected length of the longest IBD segment at a locus

Returns:

an array of inter-marker recombination probabilities

Throws:

java.lang.IllegalArgumentException - if intensity <= 0.0 || Double.isFinite(intensity)==false

java.lang.IllegalArgumentException - if this genetic map does not contain a map position for any specified marker

java.lang.NullPointerException - if markers == null