Package org.snpeff.ped
Class PlinkMap
java.lang.Object
org.snpeff.ped.PlinkMap
PLINK MAP file
References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetChrName
(int idx) getGenotypeNames
(String idStr) getId
(int idx) int
getPosition
(int idx) protected void
Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)int
size()
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Field Details
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debug
public static boolean debug
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Constructor Details
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PlinkMap
public PlinkMap() -
PlinkMap
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Method Details
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getChrName
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getGenotypeNames
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getGenotypeNames
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getId
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getPosition
public int getPosition(int idx) -
read
Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)- Parameters:
dataFileName
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size
public int size()
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