Genome scan using previously detected QTLs as covariates

Description

Use the LOD peaks previously detected in a peak object to define the additive covariates and perform a single genome scan taking cofactors into account.

Usage

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cim.peak(cross,peak)

Arguments

cross

An object of class cross. See 'qtl' package manual for read.cross function details.

peak

An object of class peak. See define.peak function for details.

Details

Performs a composite interval mapping using the scanone function with additive covariates previously defined in the related peak object. A scan is performed for traits which are affected by at least one QTL. The additive covariates for each trait are defined as the closest flanking marker to each significant LOD peak (defined in the peak feature peak\_cM). Each trait scan generates a scanone object which is concatenated to the other scanone objects.

Value

Return an object of class scanone.

Author(s)

Hamid A. Khalili

References

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890

See Also

define.peak,c.scanone,scanone,find.flanking

Examples

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data(seed10);

## Not run: seed10 <- calc.genoprob( cross=seed10, step=2, off.end=0, error.prob=0,
	 map.function='kosambi', stepwidth='fixed');
seed10 <- sim.geno( cross=seed10, step=2, off.end=0, error.prob=0,
	 map.function='kosambi', stepwidth='fixed');
## End(Not run)

out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='hk');
out.peak <- define.peak(out.em, 'all');
out.cem <- cim.peak(seed10,out.peak);

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