Rsq.2.array {eqtl}R Documentation

Add R square data to peak.array data frame

Description

Add the single QTL R square data to the related general QTL description contained within peak.array data frame.

Usage

Rsq.2.array(rsq,peak.array)

Arguments

rsq An object of classrsq. See calc.Rsq for function details.
peak.array An object of class peak.array. See peak.2.array for function details.

Details

Useful to store whole single QTL description within a simple array by adding the single QTL R square data. Add two columns containing the R square data from rsq object to the related peak.array data frame. Column Rsq contains the R square values and column RpF contains the R square significance. The R square data are computed by the function calc.Rsq.

Value

Return an object of class rsq which is a simple data frame with columns:

qtl The name of the genetic determinant. If the genetic determinant is an individual QTL, the name is formated as 'trait_name'.'chr_number'.'a number' . In the case of interactives QTL, the genetic determinant name is formated as the list of individual genetic determinant names separated by ':'.
rsq The Fisher value (set to NA if not significant: pF < th).
pF The significance (set to NA if not significant: pF < th).

Author(s)

Hamid A. Khalili

See Also

calc.Rsq,peak.2.array

Examples

data(seed10);

# Genotype probabilities
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');

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

# Computing additive effect
out.peak <- calc.adef(seed10,out.em,out.peak);

# Localizing peak
data(BSpgmap);
out.peak <- localize.qtl(seed10,out.peak,BSpgmap);
out.array <- peak.2.array(out.peak);

# R square computing
out.rsq <- calc.Rsq(seed10,out.peak);

# Adding R square data
out.array <- Rsq.2.array(out.rsq,out.array);


[Package eqtl version 1.0 Index]