cover.peak: List QTLs within a genetical region from a peak object

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

Description

List QTLs which cover a given genetical region from peak object data.

Usage

cover.peak(peak,pos,chr,pre=0)

Arguments

peak	An object of class peak. See define.peak function for details.
pos	A single numeric value : the genetic position.
chr	A single integer value : the chromosome.
pre	A single numeric value : the precision of the targeted genetic position.

Details

This function searches for the QTL from peak object which totally cover a genetical region. The targeted genetic region is defined as a single genetic position pos around which the QTLs are searched; the size of this region is defined by pre which is the max distance from pos on which the QTLs are searched. pre=0 will set to search QTLs which cover only the single genetic position pos. The QTLs are defined by LOD peaks with a support interval in a peak object.

Value

return a data frame of class peak.array

Author(s)

Hamid A. Khalili

See Also

grep,scanone,read.cross

Examples

data(seed10);

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

# return the list of QTL which colocalize at 4 cM on chromosome 3
my_peak <- cover.peak(out.peak,pos=4,chr=3,pre=0);
my_peak;

# return the list of QTL which colocalize on the genetic region 4cM-6cM
# on chromosome 4
my_peak <- cover.peak(out.peak,pos=5,chr=4,pre=1);
my_peak;

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