QTLRel (version 1.14)

lodci: Estimate LOD Support Intervals

Description

Estimate LOD support intervals.

Usage

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

Value

A data frame with the following components:

chr

The chromosome

lower

The lower bound

upper

The upper bound

index

Indicates which scanning loci

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.

Examples

data(miscEx)

if (FALSE) {
# 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)
}