Rsq.2.array: Add R square data to peak.array data frame

In eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

Description

Adds 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 is computed by the function calc.Rsq.

Value

Returns 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);

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

eqtl documentation built on May 2, 2019, 5:42 a.m.