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

Blink

R Documentation

Blink

Description

Blink

Usage

Blink(
  Y = NULL,
  QTN.position = NULL,
  GD = NULL,
  GM = NULL,
  CV = NULL,
  DPP = 1e+08,
  kinship.algorithm = "FARM-CPU",
  file.output = TRUE,
  cutOff = 0.01,
  method.GLM = "FarmCPU.LM",
  Prior = NULL,
  ncpus = 1,
  maxLoop = 10,
  LD = 0.7,
  threshold.output = 1e-04,
  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),
  WS = c(1, 1000, 10000, 1e+05, 1e+06, 1e+07),
  GP = NULL,
  FDRcut = FALSE,
  maxOut = 10,
  converge = 1,
  iteration.output = FALSE,
  acceleration = 0,
  threshold = NA,
  model = "A",
  MAF.calculate = FALSE,
  plot.style = "FarmCPU",
  p.threshold = NA,
  maf.threshold = 0,
  bound = FALSE,
  method.sub = "reward",
  method.sub.final = "reward",
  stepwise = FALSE,
  BIC.method = "naive",
  LD.wise = FALSE,
  time.cal = FALSE,
  Prediction = FALSE
)

Arguments

`Y`	= NULL, data.frame of phenotypic data, column one is sample (taxa), column two is a trait, subsequent columns are other traits.
`QTN.position`	= NULL,
`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
`CV`	= NULL, Covariates
`DPP`	= 100000000,
`kinship.algorithm`	= "FARM-CPU",
`file.output`	= TRUE,
`cutOff`	= 0.01,
`method.GLM`	= "FarmCPU.LM",
`Prior`	= NULL,
`ncpus`	= 1,
`maxLoop`	= 10,
`LD`	= 0.7,
`threshold.output`	= .0001,
`alpha`	= c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),
`WS`	= c(1e0,1e3,1e4,1e5,1e6,1e7),
`GP`	= NULL,
`FDRcut`	= FALSE,
`maxOut`	= 10,
`converge`	= 1,
`iteration.output`	= FALSE,
`acceleration`	= 0,
`threshold`	= NA,
`model`	= "A",
`MAF.calculate`	= FALSE,
`plot.style`	= "FarmCPU",
`p.threshold`	= NA,
`maf.threshold`	= 0,
`bound`	= FALSE,
`method.sub`	= "reward",
`method.sub.final`	= "reward",
`stepwise`	= FALSE,
`BIC.method`	= "naive",
`LD.wise`	= FALSE,
`time.cal`	= FALSE,
`Prediction`	= F