| summaryScantwoOld {qtl} | R Documentation |
Summarize the results of a two-dimensional genome scan
Description
Summarize the interesting aspects of the results of
scantwo; this is the version of
summary.scantwo that was included in R/qtl version
1.03 and earlier.
Usage
summaryScantwoOld(object, thresholds = c(0, 0, 0), lodcolumn=1,
type = c("joint","interaction"), ...)
Arguments
object |
An object of class |
thresholds |
A vector of length three, giving LOD thresholds for the joint LOD, interaction LOD and single-QTL conditional LOD. Negative threshold values are taken relative to the maximum joint, interaction, or individual QTL LOD, respectively. |
lodcolumn |
If the scantwo results contain LOD scores for multiple phenotypes, this argument indicates which to use in the summary. |
type |
Indicates whether to pick peaks with maximal joint or interaction LOD. |
... |
Ignored at this point. |
Details
For each pair of chromosomes, the pair of loci for which the
LOD score (either joint or interaction LOD, according to the argument
type) is a maximum is considered. The pair is printed only if
its joint LOD score exceeds the joint threshold and either (a) the
interaction LOD score exceeds its threshold or (b) both of the loci have
conditional LOD scores that are above the conditional LOD threshold,
where the conditional LOD score for locus q_1, LOD(q_1
| q_2), is the \log_{10} likelihood ratio
comparing the model with q_1 and q_2 acting
additively to the model with q_2 alone.
In the case the results of scanone are not
available, the maximum locus pair for each chromosome is printed
whenever its joint LOD exceeds the joint LOD threshold.
The criterion used in this summary is due to Gary Churchill and Śaunak Sen, and deserves careful consideration and possible revision.
Value
An object of class summary.scantwo.old, to be printed by
print.summary.scantwo.old. Pairs of loci meeting
the specified criteria are printed, with their joint LOD, interaction
LOD, and the conditional LOD for each locus, along with single-point
P-values calculated by the \chi^2 approximation.
P-values are printed as -\log_{10}(P).
If the input scantwo object does not include the results of
scanone, the interaction and conditional LOD thresholds are
ignored, and all pairs of loci for which the joint LOD exceeds its
threshold are printed, though without their conditional LOD scores.
Author(s)
Hao Wu; Karl W Broman, broman@wisc.edu; Brian Yandell
See Also
summary.scantwo,
scantwo, plot.scantwo,
max.scantwo
Examples
data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2, step=5)
out.2dim <- scantwo(fake.f2, method="hk")
# All pairs of loci
summaryScantwoOld(out.2dim)
# Pairs meeting specified criteria
summaryScantwoOld(out.2dim, c(7, 3, 3))
# Pairs with both conditional LODs > 2
summaryScantwoOld(out.2dim,c(0,1000,2))
# Pairs with interaction LOD is above 3
summaryScantwoOld(out.2dim,c(0,3,1000))