net.maizegenetics.plugindef

Class GenerateRCode

net.maizegenetics.plugindef.GenerateRCode

public class GenerateRCode

Method Detail

main

public static void main(java.lang.String[] args)

generate

public static void generate(java.lang.Class currentMatch,
                            java.lang.String inputObject,
                            java.lang.String outputObject)

genotypeTableToDosageByteArray

public static kotlin.Array[] genotypeTableToDosageByteArray(GenotypeTable genotype,
                                                            boolean useRef)

This converts a genotype table to a double dimension dosage byte array.

Parameters:

genotype - genotype table

useRef - Use reference if true, and use major allele if false

Returns:

org.jetbrains.dokka.NodeRenderContent@616cc114: byte[][] of dosage values. First index is taxa and second index is site. Byte.MIN_VALUE is used for NA

genotypeTableToSampleNameArray

public static java.lang.String[] genotypeTableToSampleNameArray(GenotypeTable genotype)

This converts the taxa of the specified genotype table to an array of taxa name strings.

Parameters:

genotype - genotype table

Returns:

org.jetbrains.dokka.NodeRenderContent@353f9bb2: string array of taxa names

genotypeTableToSampleNameArray

public static java.lang.String[] genotypeTableToSampleNameArray(TaxaList taxa)

This converts the taxa list to an array of taxa name strings.

Parameters:

taxa - taxa list

Returns:

org.jetbrains.dokka.NodeRenderContent@50a6f4fe: string array of taxa names

genotypeTableToPositionListOfArrays

public static net.maizegenetics.plugindef.GenerateRCode.PositionVectors genotypeTableToPositionListOfArrays(PositionList positions)

This converts the given position list to a @class GenerateRCode.PositionVectors

Parameters:

positions -

Returns:

org.jetbrains.dokka.NodeRenderContent@7475dbcd: @class GenerateRCode.PositionVectors

See Also:

class GenerateRCode.PositionVectors

genotypeTableToPositionListOfArrays

public static net.maizegenetics.plugindef.GenerateRCode.PositionVectors genotypeTableToPositionListOfArrays(GenotypeTable genotype)

This converts the position list of the given genotype table to a @class GenerateRCode.PositionVectors

Parameters:

genotype - genotype table

Returns:

org.jetbrains.dokka.NodeRenderContent@7396d036: @class GenerateRCode.PositionVectors

See Also:

class GenerateRCode.PositionVectors

tableReportToVectors

public static net.maizegenetics.plugindef.GenerateRCode.TableReportVectors tableReportToVectors(TableReport tableReport)

Temporary place for this experimental method.

Parameters:

tableReport -

Returns:

org.jetbrains.dokka.NodeRenderContent@3abd27fd: int[] in column order with NA set to R approach

createPhenotypeFromRDataFrameElements

public static Phenotype createPhenotypeFromRDataFrameElements(java.lang.String[] taxaArray,
                                                              java.lang.String[] colNames,
                                                              java.lang.String[] attributeType,
                                                              java.util.List dataVectors)

association

public static java.util.Map<java.lang.String,java.lang.Object> association(DistanceMatrix kinship,
                                                                           GenotypeTable genotype,
                                                                           Phenotype phenotype,
                                                                           GenotypePhenotype genoPheno,
                                                                           int minClassSize,
                                                                           boolean biallelicOnly,
                                                                           boolean appendAddDom,
                                                                           boolean saveToFile,
                                                                           java.lang.String outputFile,
                                                                           double maxP)

fastAssociation

public static java.util.Map<java.lang.String,java.lang.Object> fastAssociation(GenotypePhenotype genoPheno,
                                                                               java.lang.Double maxp,
                                                                               java.lang.Integer maxThreads,
                                                                               boolean writeToFile,
                                                                               java.lang.String outputFile)

linkageDiseq

public static TableReport linkageDiseq(GenotypeTable genotype,
                                       java.lang.String ldType,
                                       int windowSize,
                                       java.lang.String hetTreatment)

exportToFlapjack

public static void exportToFlapjack(GenotypeTable genotype,
                                    java.lang.String filename)

read

public static GenotypeTable read(java.lang.String filename,
                                 boolean keepDepth,
                                 boolean sortPositions)

genomicSelection

public static TableReport genomicSelection(Phenotype phenotype,
                                           DistanceMatrix matrix,
                                           boolean doCV,
                                           int kFolds,
                                           int nIter)

filterSitesByGRanges

public static GenotypeTable filterSitesByGRanges(GenotypeTable input,
                                                 java.lang.String[] seqName,
                                                 kotlin.Array[] start,
                                                 kotlin.Array[] end)

Filters given genotypes to only the ranges specified.

Parameters:

input - genotype table to be filtered

seqName - sequence names (i.e. chromosomes) for ranges

start - start positions for each range (inclusive)

end - end positions for each range (inclusive)

Returns:

org.jetbrains.dokka.NodeRenderContent@5d5b2550: filtered genotype table

asTasselDistanceMatrix

public static DistanceMatrix asTasselDistanceMatrix(kotlin.Array[] m,
                                                    java.lang.String[] taxa)

Convert an R matrix to a DistanceMatrix object

Parameters:

m - A numeric R matrix passed as a 2d array of doubles

taxa - A String array of taxa IDs

Returns:

org.jetbrains.dokka.NodeRenderContent@72a2685: DistanceMatrix object