QTL.gCIMapping {QTL.gCIMapping}

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)