QTL.gCIMapping: QTL Genome-Wide Composite Interval Mapping

Description Usage Arguments Details Author(s) References Examples

View source: R/QTL.gCIMapping.R

Description

Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect mixed linear model. First, each position on the genome is detected in order to construct a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid or by adaptive lasso in F2, and true QTL are identified by likelihood radio test.

Usage

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 QTL.gCIMapping(file,fileFormat,fileICIMcov,Population,Model,WalkSpeed,CriLOD,
 Likelihood,flagrqtl,DrawPlot,PlotFormat,Resolution,Trait,dir) 
 

Arguments

file

File path and name in your computer.

fileFormat

Format for input file (GCIM, ICIM, Cart).

fileICIMcov

File path and name in your computer.

Population

BC1, BC2, DH, RIL, F2.

Model

Random (random model) or Fixed (fixed model) for QTL effects.

WalkSpeed

Walk speed for Genome-wide Scanning.(WalkSpeed=1)

CriLOD

Critical LOD scores for significant QTL (CriLOD=2.5).

Likelihood

This parameter is only for F2 population, including restricted maximum likelihood (REML) and maximum likelihood (ML).

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.

Details

Package: QTL.gCIMapping
Type: Package
Version: 3.1
Date: 2018-10-16
Depends: MASS,dplyr,parcor,qtl,doParallel
Imports: methods,openxlsx,stringr,Rcpp
License: GPL version 2 or newer
LazyLoad: yes

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<[email protected]>

References

Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology. Wang Shi-Bo,Wen Yang-Jun,Ren Wen-Long,Ni Yuan-Li,Zhang Jin,Feng Jian-Ying,Zhang Yuan-Ming*

Examples

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G=data(f2data)
QTL.gCIMapping(file=f2data,fileFormat="GCIM",fileICIMcov=NULL,Population="F2",
Model="Random",WalkSpeed=1,CriLOD=2.5,Likelihood="REML",flagrqtl="FALSE",
DrawPlot="FALSE",PlotFormat="png",Resolution="Low",Trait=1,dir=tempdir()) 

QTL.gCIMapping documentation built on Oct. 17, 2018, 9:04 a.m.