tryallpositions: Test all possible positions for a marker

Description

Try all possible positions for a marker, keeping all other markers fixed, and evaluate the log likelihood and estimate the chromosome length.

Usage

tryallpositions(cross, marker, 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 a possible position for the marker. The first two columns are the chromosome ID and position. The third column is a LOD score comparing the hypotheses that the marker is in that position versus the hypothesis that it is not linked to that chromosome.

In the case of a 4-way cross, with sex.sp=TRUE, there are two additional columns with the estimated female and male genetic lengths of the respective chromosome, when the marker is in that position. With sex.sp=FALSE, or for other types of crosses, there is one additional column, with the estimated genetic length of the respective chromosome, when the marker is in that position.

The row names indicate the nearest flanking markers for each interval.

Arguments

cross: An object of class cross. See read.cross for details.
marker: Character string with name of the marker to move about.
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.

Author

Karl W Broman, broman@wisc.edu

Examples

Run this code

data(fake.bc)
tryallpositions(fake.bc, "D7M301", 7, error.prob=0, verbose=FALSE)