net.maizegenetics.analysis.gbs

Class AnnotateTOPM

net.maizegenetics.analysis.gbs.AnnotateTOPM

public class AnnotateTOPM

Methods to annotate TOPM file, including adding mapping info from aligners, adding PE tag position and genetic position, model prediction for the best position

Constructor Detail

AnnotateTOPM

public AnnotateTOPM(TagsOnPhysicalMapV3 topm)

Constructor from a TOPM file

Parameters:

topm -

Method Detail

annotateBestMappingImport

public void annotateBestMappingImport(java.lang.String indexDirS,
                                      java.lang.String predictDirS,
                                      net.maizegenetics.dna.map.TagMappingInfoV3.Aligner priorityAligner)

Import prediction result to TOPM, contain hard coding on map index

Parameters:

indexDirS -

predictDirS -

priorityAligner -

annotateBestMappingPredict

public void annotateBestMappingPredict(java.lang.String modelFileS,
                                       java.lang.String tagCountFileS,
                                       java.lang.String inputDirS,
                                       java.lang.String indexDirS,
                                       java.lang.String outputDirS)

Command line version to predict if hypotheses are correct using weka RandomForest. Make sure weka is installed (in ClassPath) in local machine Contain hard coding

Parameters:

modelFileS -

tagCountFileS -

inputDirS -

indexDirS -

outputDirS -

getNumOfRank0

public int getNumOfRank0(int tagIndex,
                         kotlin.Array[] mapIndex)

Return the number of Rank0 in an aligner

Parameters:

tagIndex -

mapIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@43d22ab:

getNumOfAlign

public int getNumOfAlign(int tagIndex,
                         kotlin.Array[] mapIndex)

Return number of alignment in an aligner

Parameters:

tagIndex -

mapIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@5f0b73f:

getPBest

public double getPBest(int tagIndex)

Return the most significant p-value across all hypotheses

Parameters:

tagIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@b5fe7e4:

getNumOfAlignAll

public int getNumOfAlignAll(int tagIndex)

Return number of alignment hypotheses across all aligners, excluding PEEnd1 and PEEnd2

Parameters:

tagIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@735e4821:

minusLog10P

public double minusLog10P(double p)

Return -log10(p-value), if p-value doesn't exist(p < 0), reutrn Double.NEGATIVE_INFINITY

Parameters:

p -

Returns:

org.jetbrains.dokka.NodeRenderContent@1e9b149b:

annotateWithBowtie2

public void annotateWithBowtie2(java.lang.String samFileS,
                                int maxMappingNum)

Annotate the TOPM file using Bowtie2

Parameters:

samFileS -

maxMappingNum - is the max number of multiple alignment

annotateWithBWA

public void annotateWithBWA(java.lang.String samFileS,
                            int maxMappingNum)

Annotate the TOPM with BWA

Parameters:

samFileS -

maxMappingNum -

annotateWithBWAMEM

public void annotateWithBWAMEM(java.lang.String samFileS,
                               int maxMappingNum)

Annotate the TOPM file using bwa-mem

Parameters:

samFileS -

maxMappingNum -

annotateWithBlastFromDir

public void annotateWithBlastFromDir(java.lang.String blastDirS,
                                     int maxMappingNum)

Annotate the TOPM with BLAST from a directory, where slices of blast result are stored

Parameters:

blastDirS -

maxMappingNum -

annotateWithBLAST

public void annotateWithBLAST(java.lang.String blastM8FileS,
                              int maxMappingNum)

Annotate the TOPM with BLAST

Parameters:

blastM8FileS -

maxMappingNum -

annotateWithPE

public void annotateWithPE(java.lang.String PETOPMFileS,
                           int maxMappingNum)

Annotate the TOPM with PE, using bowtie2 sam file

Parameters:

PETOPMFileS -

maxMappingNum -

annotateWithGMGW

public void annotateWithGMGW(java.lang.String TOGMFileS,
                             int maxMappingNum)

Annotate the TOPM with whole genome genetic mapping

Parameters:

TOGMFileS -

maxMappingNum -