lodci: Estimate LOD Support Intervals

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

Estimate LOD Support Intervals

Description

Estimate LOD support intervals.

Usage

lodci(llk, cv = 0, lod = 1.5, drop = 3)

Arguments

llk	A data frame with components (chr, dist, y, ...), where "chr" is the chromosome on which the scanning locus is located, "dist" is the genetic or physical position of the scanning locus, and "y" is the test statistic.
cv	Threshold. Reported support intervals cover at least one scanning locus where llk$y > cv.
lod	LOD (specified by lod, which is 1.5 by default) support intervals to be reported when llk$y is converted to LOD score.
drop	3 by default. See "details".

Details

In case of multiple peaks on a chromosome, a peak has to satisfy: a) above the threshold cv; b) drops, e.g., 3 LOD on both sides except chromosome ends. So if two peaks close to each other but LOD between them doesn't drop, e.g., 3 LOD, only one of them is considered.

Value

A data frame with the following components:

chr	The chromosome
lower	The lower bound
upper	The upper bound
index	Indicates which scanning loci

Examples

data(miscEx)

## Not run: 
# impute missing genotypes
pheno<- pdatF8[!is.na(pdatF8$bwt) & !is.na(pdatF8$sex),]
ii<- match(rownames(pheno), rownames(gdatF8))
geno<- gdatF8[ii,]
ii<- match(rownames(pheno), rownames(gmF8$AA))
v<- list(A=gmF8$AA[ii,ii], D=gmF8$DD[ii,ii])

gdtmp<- geno
   gdtmp<- replace(gdtmp,is.na(gdtmp),0)
# run 'genoProb'
prDat<- genoProb(gdat=gdtmp, gmap=gmapF8,
   gr=8, method="Haldane", msg=TRUE)
# estimate variance components
o<- estVC(y=pheno$bwt, x=pheno$sex, v=v)

# genome scan
llk.hk<- scanOne(y=pheno$bwt, x=pheno$sex, vc=o, prdat=prDat)

# extract LOD support intervals
tmp<- data.frame(y=llk.hk$LRT, chr=llk.hk$chr, dist=llk.hk$dist)
lodci(tmp, cv=10, lod=1.5, drop=3)

## End(Not run)

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.