peak.2.array {eqtl}R Documentation

Build a simple array from a peak object

Description

Build a simple array from a peak object.

Usage

peak.2.array(peak)

Arguments

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

Details

Useful for a genome-wide eQTL mapping. Formating the results as a simple array allow to use all classical R functions (graphical, statistical, summaries, ...) and permits all kind of manipulation for the results by the simplest way. All expression traits are represented and those which are not affected by any QTL, contain the empty data <NA> in each column.

Value

Return an object of class array.peak which is a data frame whith columns:

trait The name of the studied traits.
chr The number of the chromosome.
mname.peak The peak (pseudo-)marker name when a QTL was detected. <NA> if no QTL was detected.
lod The peak LOD score when a QTL was detected. <NA> if no QTL was detected.
peak.cM The genetic position of the peak in centiMorgan(cM) when QTL was detected. <NA> if no QTL was detected.
mname.inf The (pseudo-)marker name corresponding to the inferior SI bound when a QTL was detected. <NA> if no QTL was detected.
inf.cM The genetic position of the inferior SI bound in centiMorgan(cM) when a QTL was detected. <NA> if no QTL was detected.
mname.sup The (pseudo-)marker names corresponding to the superior SI bound when a QTL was detected. <NA> if no QTL was detected.
sup.cM The genetic position of the superior SI bound in centiMorgan(cM) if a QTL was detected. <NA> if no QTL was detected.
si.quality The subjective quality if the support interval. See 'define.peak' for details.
additive.effect The additive effects of the QTL. <NA> if no QTL has been detected.
peak.bp The physical position of the maximum LOD peak. <NA> if no QTL was detected.
inf.bp The physical position of the SI lower bound. <NA> if no QTL was detected.
sup.bp The physical position of the SI upper bound. <NA> if no QTL was detected.
type The estimated type of the eQTLs ( trans or cis for cis- and trans- eQTL respectively). <NA> if no QTL was detected or in case of non nuclear expression trait.

Author(s)

Hamid A. Khalili

See Also

scanone,read.cross

Examples

data(seed10);

# Genotype probabilities and genome scan
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');

# Defining QTLs for all traits
out.peak <- define.peak( out.em, 'all',graph=TRUE,save.pict=TRUE);

# do not run
# out.array <- peak.2.array(out.peak);

# 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);

[Package eqtl version 1.0 Index]