Estimate LOD Support Intervals
Estimate LOD support intervals.
lodci(llk, cv = 0, lod = 1.5, drop = 3)
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 |
lod |
LOD (specified by |
drop |
3 by default. See "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.
A data frame with the following components:
chr |
The chromosome |
lower |
The lower bound |
upper |
The upper bound |
index |
Indicates which scanning loci |
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)
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