summary.scanPhyloQTL {qtl} | R Documentation |
Print the maximum LOD scores for each partition on each chromosome,
from the results of scanPhyloQTL
.
## S3 method for class 'scanPhyloQTL' summary(object, format=c("postprob", "lod"), threshold, ...)
object |
An object output by the function
scanPhyloQTL . |
format |
Indicates whether to provide LOD scores or approximate posterior probabilities; see Details below. |
threshold |
A threshold determining which chromosomes should be output; see Details below. |
... |
Ignored at this point. |
This function is used to report chromosomes deemed interesting from a one-QTL
genome scan to map QTL to a phylogenetic tree (by scanPhyloQTL
).
For format="lod"
, the output contains the maximum LOD score for
each partition on each chromosome (which do not necessarily occur at
the same position). The position corresponds to the peak location for
the partition with the largest LOD score on that chromosome. The
penultimate column indicates the partition with the largest LOD
score. The final column is the difference between the LOD score for
the best partition and that for the second-best. With
format="lod"
, the threshold
argument is applied to this
last column.
For format="postprob"
, the final column contains the maximum
LOD score across partitions (and the threshold
argument is
applied to this maximum LOD score). But instead of providing the LOD
scores for each partition, these are converted to approximate
posterior probabilities under the assumption of a single diallelic QTL
on that chromosome: on each chromosome, we take
10^LOD for the partitions and rescale them to sum to 1.
An object of class summary.scanPhyloQTL
, to be printed by
print.summary.scanPhyloQTL
.
Karl W Broman, kbroman@biostat.wisc.edu
Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation.
scanPhyloQTL
, plot.scanPhyloQTL
,
max.scanPhyloQTL
, summary.scanone
,
inferredpartitions
,
simPhyloQTL
## 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)