qtl (version 1.39-5)

droponemarker: Drop one marker at a time and determine effect on genetic map

Description

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.

Usage

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)

Arguments

cross

An object of class cross. See read.cross for details.

chr

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.

error.prob

Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).

map.function

Indicates whether to use the Haldane, Kosambi, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions. (Ignored if m > 0.)

m

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.

p

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.

maxit

Maximum number of EM iterations to perform.

tol

Tolerance for determining convergence.

sex.sp

Indicates whether to estimate sex-specific maps; this is used only for the 4-way cross.

verbose

If TRUE, print information on progress; if > 1, print even more information.

Value

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.

See Also

tryallpositions, est.map, ripple, est.rf, switch.order, movemarker, drop.markers

Examples

data(fake.bc)
droponemarker(fake.bc, 7, error.prob=0, verbose=FALSE)