scantwo
; this is the version of
summary.scantwo
that was included in R/qtl version
1.03 and earlier.summaryScantwoOld(object, thresholds = c(0, 0, 0), lodcolumn=1,
type = c("joint","interaction"), ...)
scantwo
, the output of the
function scantwo
.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.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
summary.scantwo
,
scantwo
, plot.scantwo
,
max.scantwo
data(fake.f2)
fake.f2 <- subset(fake.f2, chr=c(1,6,13))
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))
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