In order to assess the support for a linkage group, this function splits the linkage groups into two pieces at each interval and in each case calculates a LOD score comparing the combined linkage group to the two pieces.
allchrsplits(cross, chr, error.prob=0.0001,
map.function=c("haldane","kosambi","c-f","morgan"),
m=0, p=0, maxit=4000, tol=1e-6, sex.sp=TRUE,
verbose=TRUE)
A data frame (actually, an object of class "scanone"
, so that
one may use plot.scanone
,
summary.scanone
, etc.) with each row being an interval
at which a split is made.
The first two columns are the chromosome ID and midpoint of the interval. The third
column is a LOD score comparing the combined linkage group to the
split into two linkage groups. A fourth column (gap
) indicates the length of
each interval.
The row names indicate the flanking markers for each interval.
An object of class cross
. See
read.cross
for details.
A vector specifying which chromosomes to study.
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 -
to have all chromosomes but those considered. A logical (TRUE/FALSE)
vector may also be used.
Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).
Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions. (Ignored if m > 0.)
Interference parameter for the chi-square model for interference; a non-negative integer, with m=0 corresponding to no interference. This may be used only for a backcross or intercross.
Proportion of chiasmata from the NI mechanism, in the Stahl model; p=0 gives a pure chi-square model. This may be used only for a backcross or intercross.
Maximum number of EM iterations to perform.
Tolerance for determining convergence.
Indicates whether to estimate sex-specific maps; this is used only for the 4-way cross.
If TRUE, print information on progress.
Karl W Broman, broman@wisc.edu
est.map
, ripple
,
est.rf
, switch.order
,
movemarker
data(fake.bc)
allchrsplits(fake.bc, 7, error.prob=0, verbose=FALSE)
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