GAPIT: GAPIT Genome Association and Prediction Integrated Tools

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

GAPIT Genome Association and Prediction Integrated Tools

Description

GAPIT analyzes phenotypic and genotypics data to infer association.

Usage

GAPIT(
  Y = NULL,
  G = NULL,
  GD = NULL,
  GM = NULL,
  KI = NULL,
  Z = NULL,
  CV = NULL,
  CV.Inheritance = NULL,
  GP = NULL,
  GK = NULL,
  testY = NULL,
  group.from = 1e+06,
  group.to = 1e+06,
  group.by = 20,
  DPP = 1e+05,
  kinship.cluster = "average",
  kinship.group = "Mean",
  kinship.algorithm = "VanRaden",
  buspred = FALSE,
  lmpred = FALSE,
  FDRcut = FALSE,
  bin.from = 10000,
  bin.to = 10000,
  bin.by = 10000,
  inclosure.from = 10,
  inclosure.to = 10,
  inclosure.by = 10,
  SNP.P3D = TRUE,
  SNP.effect = "Add",
  SNP.impute = "Middle",
  PCA.total = 0,
  SNP.fraction = 1,
  seed = NULL,
  BINS = 20,
  SNP.test = TRUE,
  SNP.MAF = 0,
  FDR.Rate = 1,
  SNP.FDR = 1,
  SNP.permutation = FALSE,
  SNP.CV = NULL,
  SNP.robust = "GLM",
  file.from = 1,
  file.to = 1,
  file.total = NULL,
  file.fragment = 99999,
  file.path = NULL,
  file.G = NULL,
  file.Ext.G = NULL,
  file.GD = NULL,
  file.GM = NULL,
  file.Ext.GD = NULL,
  file.Ext.GM = NULL,
  ngrid = 100,
  llim = -10,
  ulim = 10,
  esp = 1e-10,
  LD.chromosome = NULL,
  LD.location = NULL,
  LD.range = NULL,
  PCA.col = NULL,
  PCA.3d = FALSE,
  NJtree.group = NULL,
  NJtree.type = c("fan", "unrooted"),
  sangwich.top = NULL,
  sangwich.bottom = NULL,
  QC = TRUE,
  GTindex = NULL,
  LD = 0.1,
  plot.bin = 10^5,
  file.output = TRUE,
  cutOff = 0.05,
  Model.selection = FALSE,
  output.numerical = FALSE,
  output.hapmap = FALSE,
  Create.indicator = FALSE,
  Multi_iter = FALSE,
  num_regwas = 10,
  opt = "extBIC",
  QTN = NULL,
  QTN.round = 1,
  QTN.limit = 0,
  QTN.update = TRUE,
  QTN.method = "Penalty",
  Major.allele.zero = FALSE,
  Random.model = FALSE,
  method.GLM = "FarmCPU.LM",
  method.sub = "reward",
  method.sub.final = "reward",
  method.bin = "static",
  bin.size = c(1e+06),
  bin.selection = c(10, 20, 50, 100, 200, 500, 1000),
  memo = NULL,
  Prior = NULL,
  ncpus = 1,
  maxLoop = 3,
  threshold.output = 0.01,
  Inter.Plot = FALSE,
  Inter.type = c("m", "q"),
  WS = c(1, 1000, 10000, 1e+05, 1e+06, 1e+07),
  alpha = c(0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1),
  maxOut = 100,
  QTN.position = NULL,
  CG = NULL,
  converge = 1,
  iteration.output = FALSE,
  acceleration = 0,
  iteration.method = "accum",
  PCA.View.output = TRUE,
  Geno.View.output = TRUE,
  plot.style = "Oceanic",
  SUPER_GD = NULL,
  SUPER_GS = FALSE,
  h2 = NULL,
  NQTN = NULL,
  QTNDist = "normal",
  effectunit = 1,
  category = 1,
  r = 0.25,
  cveff = NULL,
  a2 = 0,
  adim = 2,
  Multiple_analysis = FALSE,
  model = "MLM",
  Para = NULL
)

Arguments

Y	= NULL, data.frame of phenotype data, samples in rows, traits in column, first column is sample name
G	= NULL, data.frame of genotypic data, HAPMAP format
GD	= NULL, data.frame of genetic data in 'numerical' format, samples in rows, variants in columns.
GM	= NULL, Genetic Map data.frame to provide genomic coordinates for GD
KI	= NULL, Kinship matrix
Z	= NULL,
CV	= NULL, Covariate matrix
CV.Inheritance	= NULL,
GP	= NULL,
GK	= NULL,
testY	= NULL,
group.from	= 1e+06,
group.to	= 1e+06,
group.by	= 20,
DPP	= 1e+05,
kinship.cluster	= "average", options: complete, ward, single, mcquitty, median, and centroid
kinship.group	= "Mean", options: Max, Min, and Median
kinship.algorithm	= "VanRaden", options: EMMA, Loiselle, VanRaden, Zhang
buspred	= FALSE,
lmpred	= FALSE,
FDRcut	= FALSE,
bin.from	= 10000,
bin.to	= 10000,
bin.by	= 10000,
inclosure.from	= 10,
inclosure.to	= 10,
inclosure.by	= 10,
SNP.P3D	= TRUE,
SNP.effect	= "Add",
SNP.impute	= "Middle",
PCA.total	= 0,
SNP.fraction	= 1,
seed	= NULL,
BINS	= 20,
SNP.test	= TRUE,
SNP.MAF	= 0,
FDR.Rate	= 1,
SNP.FDR	= 1,
SNP.permutation	= FALSE,
SNP.CV	= NULL,
SNP.robust	= "GLM",
file.from	= 1,
file.to	= 1,
file.total	= NULL,
file.fragment	= 99999,
file.path	= NULL,
file.G	= NULL,
file.Ext.G	= NULL,
file.GD	= NULL,
file.GM	= NULL,
file.Ext.GD	= NULL,
file.Ext.GM	= NULL,
ngrid	= 100,
llim	= -10,
ulim	= 10,
esp	= 1e-10,
LD.chromosome	= NULL,
LD.location	= NULL,
LD.range	= NULL,
PCA.col	= NULL,
PCA.3d	= FALSE,
NJtree.group	= NULL,
NJtree.type	= c("fan", "unrooted"),
sangwich.top	= NULL,
sangwich.bottom	= NULL,
QC	= TRUE,
GTindex	= NULL,
LD	= 0.1,
plot.bin	= 10^5,
file.output	= TRUE,
cutOff	= 0.05,
Model.selection	= FALSE,
output.numerical	= FALSE,
output.hapmap	= FALSE,
Create.indicator	= FALSE,
Multi_iter	= FALSE,
num_regwas	= 10,
opt	= "extBIC",
QTN	= NULL,
QTN.round	= 1,
QTN.limit	= 0,
QTN.update	= TRUE,
QTN.method	= "Penalty",
Major.allele.zero	= FALSE,
Random.model	= FALSE,
method.GLM	= "FarmCPU.LM",
method.sub	= "reward",
method.sub.final	= "reward",
method.bin	= "static",
bin.size	= c(1e+06),
bin.selection	= c(10, 20, 50, 100, 200, 500, 1000),
memo	= NULL,
Prior	= NULL,
ncpus	= 1,
maxLoop	= 3,
threshold.output	= 0.01,
Inter.Plot	= FALSE,
Inter.type	= c("m", "q"),
WS	= c(1, 1000, 10000, 1e+05, 1e+06, 1e+07),
alpha	= c(0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1),
maxOut	= 100,
QTN.position	= NULL,
CG	= NULL,
converge	= 1,
iteration.output	= FALSE,
acceleration	= 0,
iteration.method	= "accum",
PCA.View.output	= TRUE,
Geno.View.output	= TRUE,
plot.style	= "Oceanic",
SUPER_GD	= NULL,
SUPER_GS	= FALSE,
h2	= NULL,
NQTN	= NULL,
QTNDist	= "normal",
effectunit	= 1,
category	= 1,
r	= 0.25,
cveff	= NULL,
a2	= 0,
adim	= 2,
Multiple_analysis	= FALSE,
model	= "MLM", options: MLM, GLM, CMLM, MMLM, SUPER, FarmCPU, gBLUP, or cBLUP
Para	= NULL

Details

Genome Association and Prediction Integrated Tools Available models: MLM, GLM, CMLM, MMLM, SUPER, FarmCPU, gBLUP, cBLUP

Value

A list including some of the following elements:MLM, GLM, CMLM, MMLM, SUPER, FarmCPU, gBLUP, cBLUP

Author(s)

Zhiwu Zhang and Jiabo Wang

See Also

GAPIT.DP(), GAPIT.Phenotype.View(), GAPIT.judge(), GAPIT.IC(), GAPIT.SS(), GAPIT.ID().

library(help = "GAPIT3")

Examples

## Not run: 

myPhenoFile <- system.file("extdata", "mdp_traits.txt.gz", package = "GAPIT3")
myGenoFile <- system.file("extdata", "mdp_genotype_test.hmp.txt.gz", package = "GAPIT3")
myPhenotypes <- read.table(myPhenoFile, header = TRUE)
myGenotypes  <- read.table(myGenoFile, header = FALSE)

myGAPIT <- GAPIT(
  Y = myPhenotypes,
  G = myGenotypes,
  PCA.total = 3,
  file.output = FALSE,
  model = "MLM"
)

## End(Not run)

jiabowang/GAPIT3 documentation built on March 6, 2025, 2:21 a.m.