FarmCPU: FarmCPU

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

FarmCPU

Description

FarmCPU: GWAS and GS by using FarmCPU method

Usage

FarmCPU(
  Y = NULL,
  GD = NULL,
  GM = NULL,
  CV = NULL,
  GP = NULL,
  Yt = NULL,
  DPP = 1e+06,
  kinship.algorithm = "FARM-CPU",
  file.output = TRUE,
  cutOff = 0.01,
  method.GLM = "FarmCPU.LM",
  method.sub = "reward",
  method.sub.final = "reward",
  method.bin = "static",
  bin.size = c(5e+05, 5e+06, 5e+07),
  bin.selection = seq(10, 100, 10),
  memo = NULL,
  Prior = NULL,
  ncpus = 1,
  maxLoop = 10,
  threshold.output = 0.01,
  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,
  converge = 1,
  iteration.output = FALSE,
  acceleration = 0,
  model = "A",
  MAF.calculate = FALSE,
  plot.style = "FarmCPU",
  p.threshold = NA,
  QTN.threshold = 0.01,
  maf.threshold = 0.03,
  ycor = NULL,
  bound = NULL
)

Arguments

Y	= NULL, a data.frame of phenotype data, first column is sample name, second column is the trait.
GD	= NULL,
GM	= NULL,
CV	= NULL,
GP	= NULL,
Yt	= NULL,
DPP	= 1000000,
kinship.algorithm	= "FARM-CPU",
file.output	= TRUE,
cutOff	= 0.01,
method.GLM	= "FarmCPU.LM",
method.sub	= "reward",
method.sub.final	= "reward",
method.bin	= "static",
bin.size	= c(5e5,5e6,5e7),
bin.selection	= seq(10,100,10),
memo	= NULL,
Prior	= NULL,
ncpus	= 1,
maxLoop	= 10,
threshold.output	= .01,
WS	= c(1e0,1e3,1e4,1e5,1e6,1e7),
alpha	= c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),
maxOut	= 100,
QTN.position	= NULL,
converge	= 1,
iteration.output	= FALSE,
acceleration	= 0,
model	= "A",
MAF.calculate	= FALSE,
plot.style	= "FarmCPU",
p.threshold	= NA,
QTN.threshold	= 0.01,
maf.threshold	= 0.03,
ycor	= NULL,
bound	= NULL

Value

A list.

Author(s)

Xiaolei Liu and Zhiwu Zhang

Examples

## Not run: 
myPhenoFile <- system.file("extdata", "mdp_traits.txt.gz", package = "GAPIT3")
myPhenotypes <- read.table(myPhenoFile, header = TRUE)
myFarmCPU <- FarmCPU(myPhenotypes[, 1:2])

## End(Not run)

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