R: Estimate LOD Support Intervals

lodci {QTLRel} | R Documentation

## 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$y > cv`.
`lod` | `lod` (1.5 by default) LOD support intervals are reported when `llk$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, step=Inf,
       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$p, chr=llk.hk$chr, dist=llk.hk$dist)
    lodci(tmp, cv=10, lod=1.5, drop=3)

    ## End(Not run)

[Package QTLRel version 1.0 Index]