classify.qtl: Estimate the acting type of expression QTL

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

Description

Estimate wether an eQTL is cis- or trans- acting.

Usage

classify.qtl(cross, peak, etrait.coord, data.gmap)

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 for details.
etrait.coord	A data.frame with column names "etrait.name","chr","start","stop" specifying the etrait (expression trait) location on the genome: etrait.coord$array_element_name is character strings vector specifying the name of the etraits. etrait.coord$chr is a vector of integers specifying the chromosome on which the markers are localized. etrait.coord$start is a vector of integers specifying the start of the etrait's sequence in base pair. etrait.coord$stop is a vector of integers specifying the stopo of the etrait's sequence in base pair.
data.gmap	A data.frame with column names "Marker", "chr" and "PP" specifying the marker's physical location. Those ones must be the same markers defined in the related cross object. data.gmap$Marker is a vector character strings specifying the names of markers. data.gmap$chr is a vector of integers specifying the chromosomes on which the markers are localized. data.gmap$PP is a vector of integers specifying the physical marker locations on the chromosomes in base pair.

Details

Useful in the case of genome-wide expression QTL mapping. Determines cis-acting and trans-acting eQTL (or cis- and trans- eQTL) and gives a basic overview about the global eQTL network. The (potential) cis-eQTL are those which colocalize with the controlled gene. These could be typically explained by a modification within a gene promoter and therefore actually correspond to a cis-regulation (note that it would remain to be confirmed on a case by case basis: due to the lack of precision in QTLs localization for all analysis methods, a cis-acting is still biologically hypothetical; plus it could also correspond to a trans-acting eQTL localised close to its target gene). eQTLs which contains the regulated gene within their LOD support interval are classified in this category as cis. The trans-acting eQTLs are defined as those which do not colocalize with the affected gene. These could typically correspond to the mode of action of a transcription factor on the regulation of another gene's expression. eQTL which do not contain the regulated gene within their LOD support interval are classified as trans.

Value

The input peak object is returned with a component type added to the components of names(peak\$trait\$chromosome) for each previously detected QTL:

type	cis or trans for cis- and trans- eQTL respectively. <NA> if the etrait location is unknown or not nuclear.

Note

The QTL support interval locations are defined within a peak object. This classification (performed by classify.qtl) depends entirely on the support interval definition computed by the define.peak function. This function tend to underestimate cis-eQTL number as LOD-drop value are more conservative. This, however, does not replace the scientist's own manual examination of the LOD curve.

Author(s)

Hamid A. Khalili

See Also

read.cross,define.peak,calc.adef

Examples

data(seed10);

# Genotype probabilities
## 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)

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

# Additive effect computing and peaks localization
out.peak <- calc.adef(seed10,out.em,out.peak);
data(BSpgmap);
out.peak <- localize.qtl(seed10,out.peak,BSpgmap);

# Estimated actind-type of the expression QTL affecting
# the 100th expression trait and localized on chromosome 1
data(ATH.coord)
out.peak <- classify.qtl(seed10,out.peak,ATH.coord,BSpgmap);
out.peak[[26]]$'4'$type;

# idem for the trait 'CATrck'
out.peak$CATrck$'4'$type;

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