qtl (version 1.66)

allchrsplits: Test all possible splits of a chromosome into two pieces

Description

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.

Usage

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)

Value

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.

Arguments

cross

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

chr

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.

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.

Author

Karl W Broman,

See Also

est.map, ripple, est.rf, switch.order, movemarker

Examples

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