R: Partition markers into linkage groups

formLinkageGroups {qtl} | R Documentation

## Partition markers into linkage groups

### Description

Use pairwise linkage information between markers (as calculated by `est.rf` to partition markers into linkage groups.

### Usage

    formLinkageGroups(cross, max.rf=0.25, min.lod=3, reorgMarkers=FALSE,
                      verbose=FALSE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`max.rf` | Maximum recombination fraction for placing two markers in the same linkage group (see Details).
`min.lod` | Minimum LOD score for placing two markers in the same linkage group (see Details).
`reorgMarkers` | If TRUE, the output is a cross object, like the input, but with the markers organized into the inferred linkage groups. If FALSE, the output is a table indicating the initial chromosome assignments and the inferred linkage group partitions.
`verbose` | If TRUE, display information about the progress of the calculations.

### Details

Two markers are placed in the same linkage group if the estimated recombination fraction between them is <= `max.rf` and the LOD score (for the test of the rec. frac. = 1/2) is >= `min.lod`. The transitive property (if A is linked to B and B is linked to C then A is linked to C) is used to close the groups.

### Value

If `reorgMarkers=FALSE` (the default), the output is a data frame with rows corresponding to the markers and with two columns: the initial chromosome assignment and the inferred linkage group. Linkage groups are ordered by the number of markers they contain (from largest to smallest).

If `reorgMarkers=TRUE`, the output is a cross object, like the input, but with the markers reorganized into the inferred linkage groups. The marker order and marker positions within the linkage groups are arbitrary.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`est.rf`, `orderMarkers`

### Examples

    data(listeria)
    listeria <- est.rf(listeria)
    result <- formLinkageGroups(listeria)
    tab <- table(result[,1], result[,2])
    apply(tab, 1, function(a) sum(a!=0))
    apply(tab, 2, function(a) sum(a!=0))

[Package qtl version 1.41-6 Index]