net.maizegenetics.analysis.gbs

Class TagAgainstAnchor

net.maizegenetics.analysis.gbs.TagAgainstAnchor

public class TagAgainstAnchor

Constructor Detail

TagAgainstAnchor

public TagAgainstAnchor(java.lang.String hapMapHDF5,
                        java.lang.String tbtHDF5,
                        java.lang.String blockFileS,
                        java.lang.String outfileS,
                        double pThresh,
                        int minCount,
                        int coreNum,
                        int chunkSize)

Constructor to run genetic mapping on one node

Parameters:

hapMapHDF5 - anchor map, SimpleGenotypeSBit format

tbtHDF5 - TagsByTaxa of HDF5 format

blockFileS - TBTTagBlockFile, used to block the position where the tag is aligned while scanning

outfileS - output file of genetic mapping

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

chunkSize - number of tags in a chunk. This determines the time usage in a node/computer

TagAgainstAnchor

public TagAgainstAnchor(java.lang.String hapMapHDF5,
                        java.lang.String tbtHDF5,
                        java.lang.String blockFileS,
                        java.lang.String outfileS,
                        double pThresh,
                        int minCount,
                        int coreNum,
                        int chunkSize,
                        int chunkStartIndex,
                        int chunkEndIndex)

Constructor to run genetic mapping on specific chunk of TBT. This is for "qsub" in clusters.

Parameters:

hapMapHDF5 - anchor map, SimpleGenotypeSBit format

tbtHDF5 - TagsByTaxa of HDF5 format

blockFileS - TBTTagBlockFile, used to block the position where the tag is aligned while scanning

outfileS - output file of genetic mapping

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

chunkSize - number of tags in a chunk. This determines the time usage in a node/computer

chunkStartIndex - start index of chunk

chunkEndIndex - end index of chunk. Note: chunk of end index is exclusive.

Method Detail

getChunkNum

public int getChunkNum(int chunkSize)

Return the number of chunks at current chunkSize

Parameters:

chunkSize -

Returns:

org.jetbrains.dokka.NodeRenderContent@63c377a8:

getChunkNum

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

Pre-calculate number of chunks when qsub genetic mapping

Parameters:

tbtHDF5 -

chunkSize - number of tags in a chunk. This determines the time usage in a node/computer

Returns:

org.jetbrains.dokka.NodeRenderContent@e68c76f:

MTMapping

public void MTMapping(java.lang.String outfileS)

MT genetic mapping

Parameters:

outfileS -

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@556c757c:

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@77121cd0:

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@f944bad: