| drop.peakfeat {eqtl} | R Documentation |
Erase chosen peak features informations from a peak object.
drop.peakfeat(peak, feat)
peak |
An object of class peak. See define.peak function for details. |
feat |
A character string vector containing the names of the features to delete. Features could be: "additive.effect","peak.bp","inf.bp","sup.bp" or "type". See calc.adef, localize.qtl,classify.qtl functions for details. |
In peak object, QTL is defined by peak features. This function is useful to erase some peak features by avoiding to re-perform all the analyses (mainly the define.peak function). Only the peak features generated by the functions calc.adef, localize.qtl and classify.qtl should be removed. This function is used by the functions 'calc.adef', 'localize.qtl' and 'classify.qtl'.
An object of class peak
Hamid A. Khalili
define.peak,localize.qtl,calc.adef,classify.qtl
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,lodcolumn='CATrck');
out.peak <- calc.adef(seed10,out.em,out.peak)
out.peak;
data(BSpgmap);
out.peak <- localize.qtl(seed10,out.peak,BSpgmap);
out.peak;
out.peak <- drop.peakfeat(out.peak,'additive.effect');
out.peak <- drop.peakfeat(out.peak,c('inf.bp','sup.bp'));
out.peak;