| cover.peak {eqtl} | R Documentation |
List QTLs which cover a given genetical region from peak object data.
cover.peak(peak,pos,chr,pre=0)
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. |
This function searches QTL from peak object which 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 support interval in a peak object.
return a data frame of class peak.array
Hamid A. Khalili
data(seed10);
seed10 <- calc.genoprob( 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, 'all');
# return the list of QTL which colocalize at 4 cM on chromosome 3
my_peak <- cover.peak(out.peak,2,4,pre=0);
my_peak;
# return the list of QTL which colocalize on the genetic region 400-406 bp
# on chromosome 4
my_peak <- cover.peak(out.peak,pos=5,chr=4,pre=1);
my_peak;