drop.peakfeat: Erase peak features in peak object

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

Description

Erase chosen peak features informations from a peak object.

Usage

drop.peakfeat(peak, feat)

Arguments

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.

Details

In peak object, QTL is defined by peak features. This function is useful to erase some peak features by avoiding to redo 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'.

Value

An object of class peak

Author(s)

Hamid A. Khalili

See Also

define.peak,localize.qtl,calc.adef,classify.qtl

Examples

data(seed10);

out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='hk')
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;

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