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

allchrsplits {qtl} | R Documentation

## 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, broman@wisc.edu

### See Also

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

### Examples

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

[Package qtl version 1.46-2 Index]