Package vcf

Class PlinkGenMap

java.lang.Object

vcf.PlinkGenMap

All Implemented Interfaces:

GeneticMap

public final class PlinkGenMap
extends java.lang.Object
implements GeneticMap

Class PlinkGenMap represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.

Instances of class PlinkGenMap 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.
int	closestIndex(int chrom, int basePosition)	Returns the index of the genetic map position that is closest to the specified base position.
static PlinkGenMap	fromPlinkMapFile(java.io.File mapFile)	Constructs and returns a new PlinkGenMap instance from the data in the specified file.
static PlinkGenMap	fromPlinkMapFile(java.io.File mapFile, java.lang.String chrom)	Constructs and returns a new PlinkGenMap instance from the data in the specified file.
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.
int	index2BasePos(int chrom, int index)	Returns the specified base position
double	index2GenPos(int chrom, int index)	Returns the specified genetic map position
int	nMapPositions(int chrom)	Returns the number of mapped loci in this genetic map.
java.lang.String	toString()	Returns a string representation of this genetic map.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

fromPlinkMapFile

public static PlinkGenMap fromPlinkMapFile(java.io.File mapFile)

Constructs and returns a new PlinkGenMap instance from the data in the specified file.

Parameters:

mapFile - a genetic map file in PLINK format with genetic map positions in cM units

Returns:

a new PlinkGenMap instance

Throws:

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

java.lang.NullPointerException - if mapFile == null

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

fromPlinkMapFile

public static PlinkGenMap fromPlinkMapFile(java.io.File mapFile,
                                           java.lang.String chrom)

Constructs and returns a new PlinkGenMap instance from the data in the specified file. The returned genetic map will contain only positions on the specified chromosome

Parameters:

mapFile - a genetic map file in PLINK format with genetic map positions in cM units

chrom - a chromosome

Returns:

a new PlinkGenMap instance

Throws:

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

java.lang.NullPointerException - if mapFile == null || chrom == null

java.lang.NumberFormatException - if the base position on a line of the map file that corresponds to the specified chromosome is not a parsable integer

java.lang.NumberFormatException - if the genetic map position on a line of the map file that corresponds to the specified chromosome 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 the specified chromosome are not sorted in ascending order

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

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

java.lang.IllegalArgumentException - if the specified chromosome does not have at least two distinct positions in the genetic map

nMapPositions

public int nMapPositions(int chrom)

Returns the number of mapped loci in this genetic map.

Parameters:

chrom - a chromosome index

Returns:

the number of mapped loci in this genetic map

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()

index2BasePos

public int index2BasePos(int chrom,
                         int index)

Returns the specified base position

Parameters:

chrom - a chromosome index

index - a map position index

Returns:

the specified base position

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()

java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMapPositions(chrom)

index2GenPos

public double index2GenPos(int chrom,
                           int index)

Returns the specified genetic map position

Parameters:

chrom - a chromosome index

index - a map position index

Returns:

the specified genetic map position

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()

java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMapPositions(chrom)

closestIndex

public int closestIndex(int chrom,
                        int basePosition)

Returns the index of the genetic map position that is closest to the specified base position.

Parameters:

chrom - a chromosome index

basePosition - a base position

Returns:

the genetic map position index that is closes to the specified base position.

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()

genPos

public double genPos(Marker marker)

Description copied from interface: GeneticMap

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

Specified by:

genPos in interface GeneticMap

Parameters:

marker - a genetic marker

Returns:

the genetic map position of the specified marker

genPos

public double genPos(int chrom,
                     int basePosition)

Description copied from interface: GeneticMap

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

Specified by:

genPos in interface GeneticMap

Parameters:

chrom - the chromosome index

basePosition - the base coordinate on the chromosome

Returns:

the genetic map position of the specified genome coordinate

basePos

public int basePos(int chrom,
                   double geneticPosition)

Description copied from interface: GeneticMap

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.

Specified by:

basePos in interface GeneticMap

Parameters:

chrom - the chromosome index

geneticPosition - the genetic position on the chromosome

Returns:

the base position corresponding to the specified genetic map position

toString

public java.lang.String toString()

Description copied from interface: GeneticMap

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

Specified by:

toString in interface GeneticMap

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this genetic map