Description Usage Arguments Details Value Author(s) See Also Examples
List QTLs which cover a given genetical region from peak object data.
1 | cover.peak(peak,pos,chr,pre=0)
|
peak |
An object of class |
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 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.
return a data frame of class peak.array
Hamid A. Khalili
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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;
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.