net.maizegenetics.dna.map

Class TagGWASMapInfo

net.maizegenetics.dna.map.TagGWASMapInfo

public class TagGWASMapInfo

Stores variables from tag genetic mapping from GWAS. This class is used for I/O of HDF5.

Field Detail

readCount

public int readCount

Tag count in master tagCount file, unknown = Integer.MIN_VALUE

pChr

public int pChr

Physical chromosome of tag, unknown = Integer.MIN_VALUE

pPos

public int pPos

Physical position of tag, unknown = Integer.MIN_VALUE

ifMap

public boolean ifMap

If the tag is mapped by aligner

ifRef

public boolean ifRef

If the tag is reference tag

ifUnique

public boolean ifUnique

If the tag is unique to one position in genome

gChr

public int gChr

Genetic mapping chromosome of a tag, unknown = Integer.MIN_VALUE

gPos

public int gPos

Genetic mapping position of a tag, unknown = Integer.MIN_VALUE

gwasPValue

public double gwasPValue

P-value of genetic mapping of a tag

numSigSite

public int numSigSite

Total number of significant site, unknown = Integer.MIN_VALUE

tagTaxaCount

public int tagTaxaCount

Number of taxa where tag exist, unknown = Integer.MIN_VALUE

numSigChr

public int numSigChr

Total number of significant chromosome, unknown = Integer.MIN_VALUE

lRatioSB

public double lRatioSB

Likelihood ratio of the most significant chromosome Vs the second most significant chromosome, log10 value, unknown = 0

lRatioMB

public double lRatioMB

Likelihood ratio of the most significant chromosome Vs the median most significant chromosome, log10 value, unknown = 0

numSiteOnBestChrThanSecondBest

public int numSiteOnBestChrThanSecondBest

Number of site on best chromosome having more significant p value than the most significant p value on the second best chromosome, unknown = Integer.MIN_VALUE

sigSiteStart

public int sigSiteStart

Starting significant site on the best chromosome, unknown = Integer.MIN_VALUE

sigSiteEnd

public int sigSiteEnd

Ending significant site on the best chromosome, inclusive, unknown = Integer.MIN_VALUE

predictedDistance

public double predictedDistance

Predicted distance (log10 value) between mapping position and true position.

Constructor Detail

TagGWASMapInfo

public TagGWASMapInfo()

TagGWASMapInfo

public TagGWASMapInfo(int readCount,
                      int gChr,
                      int gPos,
                      double gwasPValue,
                      int numSigSite,
                      int tagTaxaCount,
                      int numSigChr,
                      double lRatioSB,
                      double lRatioMB,
                      int numSiteOnBestChrThanSecondBest,
                      int sigSiteStart,
                      int sigSiteEnd)

TagGWASMapInfo

public TagGWASMapInfo(int readCount,
                      int pChr,
                      int pPos,
                      boolean ifMap,
                      boolean ifRef,
                      boolean ifUnique,
                      int gChr,
                      int gPos,
                      double gwasPValue,
                      int numSigSite,
                      int tagTaxaCount,
                      int numSigChr,
                      double lRatioSB,
                      double lRatioMB,
                      int numSiteOnBestChrThanSecondBest,
                      int sigSiteStart,
                      int sigSiteEnd)

Method Detail

setAlignment

public void setAlignment(int pChr,
                         int pPos,
                         boolean ifMap,
                         boolean ifRef,
                         boolean ifUnique)

setPredictedDistance

public void setPredictedDistance(double predictedDistance)

isUniqueRef

public boolean isUniqueRef()

getBoxcoxAttributesStr

public java.lang.String getBoxcoxAttributesStr(kotlin.Array[] lamdas,
                                               java.lang.String delimiter)

getAttributesStr

public java.lang.String getAttributesStr(java.lang.String delimiter)