Maximum peak in genome scan to map a QTL to a phylogenetic tree
Print the chromosome with the maximum LOD score across partitions,
from the results of scanPhyloQTL.
## S3 method for class 'scanPhyloQTL'
max(object, chr, format=c("postprob", "lod"),
...)object |
An object output by the function
|
chr |
Optional vector indicating the chromosomes to consider.
This should be a vector of character strings referring to chromosomes
by name; numeric values are converted to strings. Refer to
chromosomes with a preceding |
format |
Indicates whether to provide LOD scores or approximate
posterior probabilities; see the help file for |
... |
Ignored at this point. |
The output, and the use of the argument format, is as in
summary.scanPhyloQTL.
An object of class summary.scanPhyloQTL, to be printed by
print.summary.scanPhyloQTL.
Karl W Broman, broman@wisc.edu
Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation.
## Not run:
# example map; drop X chromosome
data(map10)
map10 <- map10[1:19]
# simulate data
x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
map=map10, n.ind=150,
model=c(1, 50, 0.5, 0))
# run calc.genoprob on each cross
x <- lapply(x, calc.genoprob, step=2)
# scan genome, at each position trying all possible partitions
out <- scanPhyloQTL(x, method="hk")
# maximum peak
max(out, format="lod")
# approximate posterior probabilities at peak
max(out, format="postprob")
# all peaks above a threshold for LOD(best) - LOD(2nd best)
summary(out, threshold=1, format="lod")
# all peaks above a threshold for LOD(best), showing approx post'r prob
summary(out, format="postprob", threshold=3)
# plot of results
plot(out)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.