WenS {QTL.gCIMapping} | R Documentation |
An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2
WenS(flag,CriLOD,NUM,pheRaw,Likelihood,flagrqtl,yygg,mx,phe,chr_name,v.map, gen.raw,a.gen.orig,d.gen.orig,n,names.insert2,X.ad.tran.data,X.ad.t4,dir)
flag |
random or fix model. |
CriLOD |
LOD score. |
NUM |
the number of trait. |
pheRaw |
raw phenotype matrix . |
Likelihood |
likelihood function. |
flagrqtl |
do CIM or not. |
yygg |
covariate matrix. |
mx |
raw genotype matrix. |
phe |
phenotype matrix. |
chr_name |
chromosome name. |
v.map |
linkage map matrix. |
gen.raw |
raw genotype matrix. |
a.gen.orig |
additive genotype matrix. |
d.gen.orig |
dominant genotype matrix. |
n |
number of individual. |
names.insert2 |
linkage map after insert. |
X.ad.tran.data |
genotype matrix after insert. |
X.ad.t4 |
genotype matrix. |
dir |
file storage path. |
Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
F2=data(F2data) readraw<-Readdata(file=F2data,fileFormat="GCIM",fileICIMcov=NULL) DoResult<-Dodata(fileFormat="GCIM",Population="F2",Model="Random",readraw) WEN1re<-WenF(DoResult$pheRaw,DoResult$genRaw,DoResult$mapRaw1, DoResult$yygg1,DoResult$cov_en,WalkSpeed=1,CriLOD=2.5, dir=tempdir()) WenS(DoResult$flag,CriLOD=2.5,NUM=1,DoResult$pheRaw,Likelihood="REML", flagrqtl=FALSE,WEN1re$yygg,WEN1re$mx,WEN1re$phe,WEN1re$chr_name, WEN1re$v.map,WEN1re$gen.raw,WEN1re$a.gen.orig,WEN1re$d.gen.orig, WEN1re$n,WEN1re$names.insert2,WEN1re$X.ad.tran.data,WEN1re$X.ad.t4, dir=tempdir())