Package vcf

Interface GeneticMap

All Known Implementing Classes:

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.
static double[]	genPos(GeneticMap genMap, double minGenDist, Markers markers)	Returns the an array of length markers.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
static double[]	genPos(GeneticMap genMap, Markers markers)	Returns the an array of length markers.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
double	genPos(Marker marker)	Returns the genetic map position of the specified marker.
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

static double[] genPos(GeneticMap genMap,
                       Markers markers)

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

Parameters:

genMap - the genetic map

markers - the list of markers

Returns:

an array of genetic map positions

Throws:

java.lang.IllegalArgumentException - if markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()

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

java.lang.NullPointerException - if genMap == null || markers == null

genPos

static double[] genPos(GeneticMap genMap,
                       double minGenDist,
                       Markers markers)

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

Parameters:

genMap - the genetic map in cM units

minGenDist - the required minimum cM distance between successive markers

markers - the list of markers

Returns:

an array of genetic map positions

Throws:

java.lang.IllegalArgumentException - if markers.marker(0).chromIndex() != markers.marker(markers.nMarkers() - 1).chromIndex()

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

java.lang.IllegalArgumentException - if Double.isFinite(minDist) == false

java.lang.NullPointerException - if genMap == null || markers == null