summary.scantwo {qtl} | R Documentation |
Summarize the interesting aspects of the results of scantwo
.
summary.scantwo(object, thresholds, ...)
object |
An object of class scantwo , the output of the
function scantwo . |
thresholds |
A vector of length three, giving LOD thresholds for the joint LOD, interaction LOD and single-QTL conditional LOD. |
... |
Ignored at this point. |
For each pair of chromosomes, the pair of loci for which the joint LOD score 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 q1, LOD(q1 | q2), is the log10 likelihood ratio comparing the model with q1 and q2 acting additively to the model with q2 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 Saunak Sen, and deserves careful consideration and possible revision.
An object of class summary.scantwo
, to be printed by
print.summary.scantwo
. 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-square approximation. P-values
are printed as -log10(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.
Hao Wu, hao@jax.org; Karl W Broman, kbroman@jhsph.edu
scantwo
, plot.scantwo
,
max.scantwo
data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=5) out.2dim <- scantwo(fake.f2, method="hk", chr=c(1,6,13)) # All pairs of loci summary(out.2dim) # Pairs meeting specified criteria summary(out.2dim, c(7, 3, 3)) # Pairs with both conditional LODs > 2 summary(out.2dim,c(0,1000,2)) # Pairs with interaction LOD is above 3 summary(out.2dim,c(0,3,1000))