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

In kbroman/qtl: Tools for Analyzing QTL Experiments

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)

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.

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.

Author(s)

Karl W Broman, [e-mail]

See Also

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

Examples

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

kbroman/qtl documentation built on Aug. 26, 2024, 12:33 a.m.