qtl: find.pseudomarker – R documentation

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qtl

find.pseudomarker

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

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")

qtl

Tools for Analyzing QTL Experiments

v1.48-1

GPL-3

Authors

Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, Brian Yandell, and R Core Team

Initial release

2021-03-24