| bayesint {qtl} | R Documentation |
Calculate an approximate Bayesian credible interval for a particular
chromosome, using output from scanone.
bayesint(results, chr, qtl.index, prob=0.95, lodcolumn=1, expandtomarkers=FALSE)
results |
Output from scanone, or a qtl object
as output from refineqtl. |
chr |
A chromosome ID (if input results are from
scanone. |
qtl.index |
Numeric index for a QTL (if input results are
from refineqtl. |
prob |
Probability coverage of the interval. |
lodcolumn |
An integer indicating which
of the LOD score columns should be considered (if input
results are from scanone). |
expandtomarkers |
If TRUE, the interval is expanded to the nearest flanking markers. |
We take 10^LOD, rescale it to have area 1, and then calculate the connected interval with density above some threshold and having coverage matching the target probability.
An object of class scanone indicating the
estimated QTL position and the approximate endpoints
for the Bayesian credible interval.
Karl W Broman, kbroman@biostat.wisc.edu
data(hyper) hyper <- calc.genoprob(hyper, step=0.5) out <- scanone(hyper, method="hk") bayesint(out, chr=1) bayesint(out, chr=4) bayesint(out, chr=4, prob=0.99) bayesint(out, chr=4, expandtomarkers=TRUE)