| add.threshold {qtl} | R Documentation |
Add a significance threshold to a plot created by
plot.scanone), using the permutation results.
add.threshold(out, chr, perms, alpha=0.05, lodcolumn=1, gap=25, ...)
out |
An object of class "scanone", as output by
scanone. This must be identical to what was used
in the call to plot.scanone. |
chr |
Optional vector specifying which chromosomes to plot. If a selected subset of chromosomes were plotted, they must be specified here. |
perms |
Permutation results from scanone, used
to calculate the significance threshold. |
alpha |
Significance level of the threshold. |
lodcolumn |
An integer indicating which of column in the permutation results should be used. |
gap |
Gap separating chromosomes (in cM). This must be identical
to what was used in the call to plot.scanone. |
... |
Passed to the function abline when it
is called. |
This function allows you to add a horizontal line at the significance
threshold to genome scan results plotted by
plot.scanone.
The arguments out, chr, and gap must match what
was used in the call to plot.scanone.
The argument perms must be specified. If X-chromosome-specific
permutations were performed (via the argument perm.Xsp in the
call to scanone), separate thresholds will be
plotted for the autosomes and the X chromosome. These are calculated
via the summary.scanoneperm function.
None.
Karl W Broman, kbroman@biostat.wisc.edu
scanone,
plot.scanone,
summary.scanoneperm
data(hyper)
hyper <- calc.genoprob(hyper)
out <- scanone(hyper, method="hk")
operm <- scanone(hyper, method="hk", n.perm=100, perm.Xsp=TRUE)
plot(out, chr=c(1,4,6,15,"X"))
add.threshold(out, chr=c(1,4,6,15,"X"), perms=operm, alpha=0.05)
add.threshold(out, chr=c(1,4,6,15,"X"), perms=operm, alpha=0.1,
col="green", lty=2)