R: Find the pseudomarker closest to a specified position

find.pseudomarker {qtl} | R Documentation

## Find the pseudomarker closest to a specified position

### Description

Find the pseudomarker closest to a specified position on a chromosome.

### Usage

    find.pseudomarker(cross, chr, pos, where=c("draws", "prob"), addchr=TRUE)

### 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.
`where` | Indicates whether to look in the `draws` or `prob` components of the input cross.
`addchr` | If TRUE, include something like `"c5."` at the beginning of the names of non-pseudomarker locations, as in the output of `scanone`; if FALSE, don't include this sort of string, as in the genotype probabilities from `calc.genoprob`.

### Details

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

If 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, the input positions are assumed to correspond to the female genetic map.

### Value

A vector of pseudomarker names (of the same length as the input `pos`), corresponding to the markers nearest to the specified chromosomes/positions.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

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

### Examples

    data(listeria)
    listeria <- calc.genoprob(listeria, step=2.5)
    find.pseudomarker(listeria, 5, 28, "prob")
    find.pseudomarker(listeria, c(1, 5, 13), c(81, 28, 26), "prob")

[Package qtl version 1.46-2 Index]