GENESIS/NAMESPACE at master · hanchenphd/GENESIS · GitHub

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import(grDevices)
import(graphics)
importFrom(methods, as)
import(stats)
importFrom(utils, read.table)

import(Biobase)
import(gdsfmt)
import(graph)

importFrom(GWASTools, GdsGenotypeReader, GenotypeData)
importClassesFrom(GWASTools,
                  GdsGenotypeReader,
                  GenotypeData,
                  ScanAnnotationDataFrame)
importMethodsFrom(GWASTools,
                  close,
                  getChromosome,
                  getGenotypeSelection,
                  getPosition,
                  getScanID,
                  getSnpID,
                  getVariable,
                  getSex,
                  hasSex,
                  XchromCode,
                  YchromCode)

import(SeqArray)
importFrom(SeqVarTools, SeqVarData)
importClassesFrom(SeqVarTools, SeqVarData)
importMethodsFrom(SeqVarTools,
                  altDosage,
                  alleleDosage,
                  sampleData,
                  variantData)

importFrom(BiocGenerics, start, end)
importFrom(GenomicRanges, GRanges)
importFrom(IRanges, IRanges, findOverlaps)
importFrom(S4Vectors, queryHits, subjectHits)

export(admixMapMM,
       assocTestMM,
       assocTestSeq,
       assocTestSeqWindow,
       fitNullMM,
       fitNullReg,
       king2mat,
       pcair,
       pcairPartition,
       pcrelate,
       pcrelateMakeGRM,
       pcrelateReadInbreed,
       pcrelateReadKinship,
       varCompCI)

S3method(plot, pcair)
S3method(summary, pcair)
S3method(print, pcair)
S3method(print, summary.pcair)