In knausb/GAPIT3documentation: Documentation for GAPIT3

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(GAPIT3documentation)
knitr::opts_chunk$set(fig.align = "center")

Load example data.

myPhenoFile <- system.file("extdata", "mdp_traits.txt.gz",
                    package = "GAPIT3documentation")
myGenoFile <- system.file("extdata", "mdp_genotype_test.hmp.txt.gz",
                    package = "GAPIT3documentation")

myPhenotypes <- read.table(myPhenoFile, header = TRUE)
myGenotypes  <- read.table(myGenoFile, header = FALSE)

head(myPhenotypes)
myGenotypes[1:4, 1:9]

From GAPIT.R we have the first call to GAPIT.DP.

DP = GAPIT.DP(G=G, GD=GD, GM=GM, KI=KI0, Z=Z, CV=CV,
              CV.Inheritance = Para$CV.Inheritance, 
              GP = GP,
              GK = GK,
              group.from = Para$group.from, 
              group.to = Para$group.to,
              group.by = Para$group.by,
              DPP = Para$DPP, 
              FDRcut = Para$FDRcut,
              kinship.cluster = Para$kinship.cluster,
              kinship.group = Para$kinship.group,
              kinship.algorithm = Para$kinship.algorithm,
              NJtree.group = Para$NJtree.group,
              NJtree.type = Para$NJtree.type,
              plot.bin = Para$plot.bin, 
              PCA.col = Para$PCA.col,
              PCA.3d = Para$PCA.3d,
              sangwich.top = Para$sangwich.top,
              sangwich.bottom = Para$sangwich.bottom,
              LD=Para$LD,bin.from = Para$bin.from,
              bin.to = Para$bin.to,
              bin.by = Para$bin.by,
              inclosure.from = Para$inclosure.from,
              inclosure.to = Para$inclosure.to,
              inclosure.by = Para$inclosure.by,
              SNP.P3D = Para$SNP.P3D,
              SNP.effect = Para$SNP.effect,
              SNP.impute = Para$SNP.impute,
              PCA.total = Para$PCA.total, 
              SNP.fraction = Para$SNP.fraction, 
              seed = Para$seed,
              BINS = Para$BINS,
              SNP.test=Para$SNP.test,
              SNP.MAF= Para$SNP.MAF,
              FDR.Rate = Para$FDR.Rate, 
              SNP.FDR = Para$SNP.FDR,
              SNP.permutation = Para$SNP.permutation,
              opt = Para$opt,
              SNP.CV = Para$SNP.CV,
              SNP.robust = Para$SNP.robust,
              Inter.Plot = Para$Inter.Plot,
              Inter.type = Para$Inter.type,
              file.from = Para$file.from, 
              file.to = Para$file.to,
              file.total= Para$file.total,
              file.fragment = Para$file.fragment,
              file.path = Para$file.path,
              file.G = Para$file.G, 
              file.Ext.G= Para$file.Ext.G,
              file.GD = Para$file.GD,
              file.GM = Para$file.GM, 
              file.Ext.GD = Para$file.Ext.GD,
              file.Ext.GM = Para$file.Ext.GM,
              ngrid = Para$ngrid,
              llim = Para$llim,
              ulim = Para$ulim, 
              esp = Para$esp,
              Multi_iter = Para$Multi_iter,
              num_regwas = Para$num_regwas,
              LD.chromosome = Para$LD.chromosome,
              LD.location = Para$LD.location,
              LD.range = Para$LD.range,
              QC = Para$QC,
              GTindex = Para$GTindex,
              cutOff = Para$cutOff,
              Model.selection = Para$Model.selection,
              output.numerical = Para$output.numerical,
              Random.model = Para$Random.model,
              Create.indicator = Para$Create.indicator,
              QTN = Para$QTN, 
              QTN.round = Para$QTN.round,
              QTN.limit = Para$QTN.limit,
              QTN.update = Para$QTN.update,
              QTN.method = Para$QTN.method, 
              Major.allele.zero = Para$Major.allele.zero,
              method.GLM = Para$method.GLM,
              method.sub = Para$method.sub,
              method.sub.final = Para$method.sub.final,
              method.bin = Para$method.bin,
              bin.size = Para$bin.size,
              bin.selection = Para$bin.selection,
              memo = Para$memo,
              Prior = Para$Prior,
              ncpus = Para$ncpus,
              maxLoop = Para$maxLoop,
              threshold.output = Para$threshold.output,
              WS = Para$WS,
              alpha = Para$alpha,
              maxOut = Para$maxOut,
              QTN.position = Para$QTN.position,
              converge = Para$converge,
              iteration.output = Para$iteration.output,
              acceleration = Para$acceleration,
              iteration.method = Para$iteration.method,
              PCA.View.output = Para$PCA.View.output,
              output.hapmap = Para$output.hapmap, 
              file.output = Para$file.output,
              Geno.View.output = Para$Geno.View.output,
              plot.style = Para$plot.style,
              SUPER_GD = Para$SUPER_GD,
              SUPER_GS = Para$SUPER_GS,
              CG = Para$CG,
              model = model
)

GAPIT.DP calls GAPIT.Genotype

myGenotype <- GAPIT.Genotype(G = G,
                             GD = GD,
                             GM = GM,
                             KI = KI,
                             PCA.total = PCA.total,
                             kinship.algorithm = kinship.algorithm,
                             SNP.fraction = SNP.fraction, 
                             SNP.test = FALSE,
                             file.path = file.path,
                             file.from = file.from,
                             file.to = file.to,
                             file.total = file.total,
                             file.fragment = file.fragment, 
                             file.G = file.G,
                             file.Ext.G = file.Ext.G,
                             file.GD = file.GD, 
                             file.GM = file.GM,
                             file.Ext.GD = file.Ext.GD,
                             file.Ext.GM = file.Ext.GM,
                             SNP.MAF = SNP.MAF,
                             FDR.Rate = FDR.Rate,
                             SNP.FDR = SNP.FDR,
                             SNP.effect = SNP.effect,
                             SNP.impute = SNP.impute,
                             NJtree.group = NJtree.group,
                             NJtree.type = NJtree.type,
                             LD.chromosome = LD.chromosome,
                             LD.location = LD.location,
                             LD.range = LD.range,
                             GP = GP, 
                             GK = GK,
                             bin.size = NULL,
                             inclosure.size = NULL, 
                             sangwich.top = sangwich.top,
                             sangwich.bottom = sangwich.bottom,
                             GTindex = NULL,
                             file.output = file.output,
                             Create.indicator = Create.indicator,
                             Major.allele.zero = Major.allele.zero,
                             Geno.View.output = Geno.View.output,
                             PCA.col=PCA.col,
                             PCA.3d=PCA.3d
                )