Description Usage Arguments Value Author(s) See Also Examples
Determines distance between position of maximum LOD score and trait position, based on annotation. Assigns CIS/Trans status based on a window size (default=5)
1 | peaks(maxlod.out, sigpos.out, annot, win = 5)
|
maxlod.out |
Output from |
sigpos.out |
Output from |
annot |
A data.frame consisting of two columns:
|
win |
Window size, in same units as |
Returns a list corresponding to the number of chromosomes:
maxpos |
List of maximum LOD positions, named by trait, with existing location in annotation |
maxlods |
List of maximum LOD scores, named by trait, with existing location in annotation |
maxpos.cis |
List of maximum LOD positions, named by trait, within +/- 1/2 window size of annotation location |
maxpos.vaguelycis |
List of maximum LOD positions, named by trait, on the same chromosome as annotation location |
maxpos.forsuretrans |
List of maximum LOD positions, named by trait, on different chromosome as annotation location |
maxpos.trans |
List of maximum LOD positions, named by trait, outside of +/- 1/2 window size, or on different chromosome of annotation location |
maxlods.cis |
List of maximum LOD scores, named by trait, within +/- 1/2 window size of annotation location |
maxlods.trans |
List of maximum LOD scores, named by trait, outside of +/- 1/2 window size, or on different chromosome of annotation location |
maxpos.trait |
List of annotation positions, named by trait |
peaks |
|
Karl W. Broman and Aimee Teo Broman
1 2 3 4 5 6 7 8 9 10 11 | data(fake.f2expr)
fake.f2expr <- calc.genoprob(fake.f2expr)
scan.f2 <- scanone(fake.f2expr,pheno.col=1:100, method="hk")
maxlod.f2 <- maxlod(scan.f2)
sigpos.f2 <- maxlod.sigpos(maxlod.f2,sig.lod=3)
## Fake annotation ##
data(fake.annot)
peaks.f2 <- peaks(maxlod.f2,sigpos.f2,fake.annot)
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