map.peak {eqtl}R Documentation

Resume maximum LOD peak position from peak object

Description

Resume all maximum LOD peaks position from peak object as a data frame. This function is useful for Composite Interval Mapping to define as co-factor previoulsy detected QTLs.

Usage

map.peak(peak)

Arguments

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

Details

Resume all detected QTLs location from peak object as a data frame. This function could be used by the function wash.covar and gives an overview of the covariates which can be used for a Composite Interval Mapping.

Value

Returns a data frame with columns:

trait The names of the affected traits.
chr The names of the chromosomes on which the QTL has been detected.
cM The genetic position of the detected QTL.

Author(s)

Hamid A. Khalili

See Also

define.peak

Examples

        data(seed10);

        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');

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

        covar <- map.peak(out.peak);

        covar;

[Package eqtl version 1.0 Index]