GAPIT.Main: GAPIT.Main
In jiabowang/GAPIT3: GAPIT (Genomic Association and Prediction Integrated Tool)

GAPIT.Main

R Documentation

GAPIT.Main

Description

GAPIT.Main

Usage

GAPIT.Main(
  Y,
  G = NULL,
  GD = NULL,
  GM = NULL,
  KI = NULL,
  Z = NULL,
  CV = NULL,
  CV.Inheritance = NULL,
  SNP.P3D = TRUE,
  GP = NULL,
  GK = NULL,
  group.from = 1e+06,
  group.to = 1,
  group.by = 10,
  kinship.cluster = "average",
  kinship.group = "Mean",
  kinship.algorithm = NULL,
  DPP = 50000,
  ngrid = 100,
  llin = -10,
  ulim = 10,
  esp = 1e-10,
  GAPIT3.output = TRUE,
  file.path = NULL,
  file.from = NULL,
  file.to = NULL,
  file.total = NULL,
  file.fragment = 512,
  file.G = NULL,
  file.Ext.G = NULL,
  file.GD = NULL,
  file.GM = NULL,
  file.Ext.GD = NULL,
  file.Ext.GM = NULL,
  SNP.MAF = 0,
  FDR.Rate = 1,
  SNP.FDR = 1,
  SNP.effect = "Add",
  SNP.impute = "Middle",
  PCA.total = 0,
  GAPIT.Version = GAPIT.Version,
  name.of.trait,
  GT = NULL,
  SNP.fraction = 1,
  seed = 123,
  BINS = 20,
  SNP.test = TRUE,
  SNP.robust = "FaST",
  LD.chromosome = NULL,
  LD.location = NULL,
  LD.range = NULL,
  model = model,
  bin.from = 10000,
  bin.to = 5e+06,
  bin.by = 1000,
  inclosure.from = 10,
  inclosure.to = 1000,
  inclosure.by = 10,
  SNP.permutation = FALSE,
  SNP.CV = NULL,
  NJtree.group = NJtree.group,
  NJtree.type = NJtree.type,
  plot.bin = plot.bin,
  genoFormat = NULL,
  hasGenotype = NULL,
  byFile = NULL,
  fullGD = NULL,
  PC = NULL,
  GI = NULL,
  Timmer = NULL,
  Memory = NULL,
  sangwich.top = NULL,
  sangwich.bottom = NULL,
  QC = TRUE,
  GTindex = NULL,
  LD = 0.05,
  file.output = TRUE,
  cutOff = 0.05,
  Model.selection = FALSE,
  Create.indicator = FALSE,
  QTN = NULL,
  QTN.round = 1,
  QTN.limit = 0,
  QTN.update = TRUE,
  QTN.method = "Penalty",
  Major.allele.zero = FALSE,
  QTN.position = NULL,
  SUPER_GD = NULL,
  SUPER_GS = SUPER_GS,
  plot.style = "Beach",
  CG = CG,
  chor_taxa = chor_taxa
)

Arguments

`Y`	data.frame of phenotype data, samples in rows, traits in columns
`G`	data.frame of genotypic data, HAPMAP format
`GD`	data.frame of genotypic data
`GM`	genetic map for GD
`KI`	param
`Z`	param
`CV`	param
`CV.Inheritance`	param
`SNP.P3D`	param
`GP`	param
`GK`	param
`group.from`	param
`group.to`	param
`group.by`	param
`kinship.cluster`	param
`kinship.group`	param
`kinship.algorithm`	param
`DPP`	param
`ngrid`	param
`llin`	param
`ulim`	param
`esp`	param
`GAPIT3.output`	param
`file.path`	param
`file.from`	param
`file.to`	param
`file.total`	param
`file.fragment`	param
`file.G`	param
`file.Ext.G`	param
`file.GD`	param
`file.GM`	param
`file.Ext.GD`	param
`file.Ext.GM`	param
`SNP.MAF`	param
`FDR.Rate`	param
`SNP.FDR`	param
`SNP.effect`	param
`SNP.impute`	param
`PCA.total`	param
`GAPIT.Version`	param
`name.of.trait`	param
`GT`	param
`SNP.fraction`	param
`seed`	param
`BINS`	param
`SNP.test`	param
`SNP.robust`	param
`LD.chromosome`	param
`LD.location`	param
`LD.range`	param
`model`	param
`bin.from`	param
`bin.to`	param
`bin.by`	param
`inclosure.from`	param
`inclosure.to`	param
`inclosure.by`	param
`SNP.permutation`	param
`SNP.CV`	param
`NJtree.group`	param
`NJtree.type`	param
`plot.bin`	param
`genoFormat`	param
`hasGenotype`	param
`byFile`	param
`fullGD`	param
`PC`	param
`GI`	param
`Timmer`	param
`Memory`	param
`sangwich.top`	param
`sangwich.bottom`	param
`QC`	param
`GTindex`	param
`LD`	param
`file.output`	param
`cutOff`	param
`Model.selection`	param
`Create.indicator`	param
`QTN`	param
`QTN.round`	param
`QTN.limit`	param
`QTN.update`	param
`QTN.method`	param
`Major.allele.zero`	param
`QTN.position`	param
`SUPER_GD`	param
`SUPER_GS`	param
`plot.style`	param
`CG`	param
`chor_taxa`	param