net.maizegenetics.analysis.gbs

Class TagAgainstAnchorHypothesis

net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis

public class TagAgainstAnchorHypothesis

Constructor Detail

TagAgainstAnchorHypothesis

public TagAgainstAnchorHypothesis(java.lang.String hapMapHDF5,
                                  java.lang.String tbtHDF5,
                                  java.lang.String topmFileS,
                                  java.lang.String software,
                                  int testSiteNum,
                                  double pThresh,
                                  int minCount,
                                  int coreNum)

Constructor to run genetic mapping

Parameters:

hapMapHDF5 - anchor map

tbtHDF5 - TagsByTaxa of HDF5 format

pThresh - P-value threshold, default: 1e-6

minCount - minimum count when tag appear in taxa (In TBT file), default = 20, too low number lacks statistical power

coreNum - default:-1, which means using all cores in a node. When the coreNum is set less than total core number, which means using coreNum cores, each core runs 1 thread

Method Detail

getChunkNum

public static int getChunkNum(java.lang.String tbtHDF5,
                              int chunkSize)

Pre-calculate number of chunks when qsub genetic mapping

Parameters:

tbtHDF5 -

Returns:

org.jetbrains.dokka.NodeRenderContent@750f07ed:

MTMapping

public void MTMapping()

MT genetic mapping

fastTestSites

public double fastTestSites(OpenBitSet obsTdist,
                            OpenBitSet obsMajor,
                            OpenBitSet obsMinor,
                            double maf,
                            cern.jet.random.Binomial binomFunc)

fast test, using ratio to reduce the calculation of binomial and p (reduce 73%), but the time is only saved by 3%

Parameters:

obsTdist -

obsMajor -

obsMinor -

maf -

binomFunc -

Returns:

org.jetbrains.dokka.NodeRenderContent@4c3820ed:

testSites

public double testSites(OpenBitSet obsTdist,
                        OpenBitSet obsMajor,
                        OpenBitSet obsMinor,
                        double maf,
                        cern.jet.random.Binomial binomFunc)

Test association using binomial test, collecting P-value

Parameters:

obsTdist -

obsMajor -

obsMinor -

binomFunc -

Returns:

org.jetbrains.dokka.NodeRenderContent@7ca46a13:

testSites

public static double testSites(OpenBitSet obsTdist,
                               OpenBitSet obsMajor,
                               OpenBitSet obsMinor,
                               cern.jet.random.Binomial binomFunc)

Test association using binomial test, collecting P-value

Parameters:

obsTdist -

obsMajor -

obsMinor -

binomFunc -

Returns:

org.jetbrains.dokka.NodeRenderContent@43450851: