R: Find marker closest to a specified position

find.marker {qtl} | R Documentation

## Find marker closest to a specified position

### Description

Find the genetic marker closest to a specified position on a chromosome.

### Usage

    find.marker(cross, chr, pos, index)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`chr` | A vector of chromosome identifiers, or a single such.
`pos` | A vector of cM positions.
`index` | A vector of numeric indices of the markers within chromosomes.

### Details

Provide one of `pos` or `index`.

If the input `chr` has length one, it is expanded to the same length as the input `pos` or `index`.

If `pos` is specified and multiple markers are exactly the same distance from the specified position, one is chosen at random from among those with the most genotype data.

For a cross with sex-specific maps, positions specified by `pos` are assumed to correspond to the female genetic map.

### Value

A vector of marker names (of the same length as the input `pos`), corresponding to the markers nearest to the specified chromosomes/positions (if `pos` is specified) or to the input numeric indices (in `index` is specified).

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`find.flanking`, `plotPXG`, `find.pseudomarker`, `effectplot`, `find.markerpos`

### Examples

    data(listeria)
    find.marker(listeria, 5, 28)
    find.marker(listeria, 5, index=6)
    find.marker(listeria, c(1, 5, 13), c(81, 28, 26))

[Package qtl version 1.46-2 Index]