Drop one marker at a time from a genetic map and calculate the change in log likelihood and in the chromosome length, in order to identify problematic markers.
droponemarker(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 a marker.
The first two columns are the chromosome ID and position. The third
column is a LOD score comparing the hypothesis that the marker is not
linked to the hypothesis that it belongs at that position.
In the case of a 4-way cross, with sex.sp=TRUE
, there are two
additional columns with the change in the estimated female and male genetic lengths
of the respective chromosome, upon deleting that marker.
With sex.sp=FALSE
, or for other types of crosses, there is one
additional column, with the change in estimated genetic length of the respective
chromosome, when the marker is omitted.
A well behaved marker will have a negative LOD score and a small change in estimated genetic length. A poorly behaved marker will have a large positive LOD score and a large change in estimated genetic length. But note that dropping the first or last marker on a chromosome could result in a large change in estimated length, even if they are not badly behaved; for these markers one should focus on the LOD scores, with a large positive LOD score being bad.
An object of class cross
. See
read.cross
for details.
A vector specifying which chromosomes to test for the
position of the marker. 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; if > 1, print even more information.
Karl W Broman, broman@wisc.edu
tryallpositions
, est.map
, ripple
,
est.rf
, switch.order
,
movemarker
, drop.markers
data(fake.bc)
droponemarker(fake.bc, 7, error.prob=0, verbose=FALSE)
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