QTL.gCIMapping: QTL Genome-Wide Composite Interval Mapping

In QTL.gCIMapping: QTL Genome-Wide Composite Interval Mapping

QTL Genome-Wide Composite Interval Mapping

Description

QTL Genome-Wide Composite Interval Mapping

Usage

QTL.gCIMapping(
  file = NULL,
  fileFormat = "GCIM",
  filecov = NULL,
  MCIMmap = NULL,
  Population = NULL,
  method = "GCIM-QEI",
  MultiEnv = FALSE,
  Model = "Random",
  WalkSpeed = 1,
  CriLOD = 3,
  CriDis = 5,
  Likelihood = "REML",
  SetSeed = 11001,
  flagrqtl = FALSE,
  DrawPlot = TRUE,
  PlotFormat = "jpeg",
  Resolution = "Low",
  Trait = NULL,
  dir = NULL,
  CLO = NULL
)

Arguments

file	File path and name in your computer.
fileFormat	Format for input file: GCIM, ICIM, Cart, or MCIM.
filecov	Covariate file of QTLIciMapping or QTLNetwork.
MCIMmap	Map file of QTLNetwork.
Population	Population type: F2, BC1, BC2, DH, RIL.
method	Method "GCIM" or method "GCIM-QEI".
MultiEnv	Whether to perform multi-environment analysis.
Model	Random or fixed model.
WalkSpeed	Walk speed for Genome-wide Scanning.
CriLOD	Critical LOD scores for significant QTL.
CriDis	The distance of optimization.
Likelihood	This parameter is only for F2 population,including REML (restricted maximum likelihood ) and ML(maximum likelihood).
SetSeed	In which the cross validation experiment is needed. Generally speaking, the random seed in the cross-validation experiment was set as 11001. If some known genes are not identified by the seed, users may try to use some new random seeds. At this case, one better result may be obtained.
flagrqtl	This parameter is only for F2 population, flagrqtl="FALSE" in the first running. If the other software detects only one QTL in a neighborhood but this software finds two linked QTLs (one with additive effect and another with dominant effect) in the region, let flagrqtl="TRUE"
DrawPlot	This parameter is for all the populations, including FALSE and TRUE, DrawPlot=FALSE indicates no figure output, DrawPlot=TRUE indicates the output of the figure against genome position.
PlotFormat	This parameter is for all the figure files, including *.jpeg, *.png, *.tiff and *.pdf.
Resolution	This parameter is for all the figure files, including Low and High.
Trait	Trait=1:3 indicates the analysis from the first trait to the third trait.
dir	This parameter is for the save path.
CLO	Number of CPUs.

Examples

data(F2data)
QTL.gCIMapping(file=F2data,Population="F2",
MultiEnv=TRUE,Model="Random",CriLOD=3,
Trait=1,dir=tempdir(),CLO=2)

QTL.gCIMapping documentation built on March 18, 2022, 5:54 p.m.