qtl: replacemap.scantwo – R documentation

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replacemap.scantwo

Replace the genetic map in QTL mapping results with an alternate map

Description

Replace the positions of LOD scores in output from scantwo with values based on an alternative map (such as a physical map), with pseudomarker locations determined by linear interpolation.

Usage

## S3 method for class 'scantwo'
replacemap(object, map)

Arguments

`object`	An object of class `"scantwo"`, as output by the function `scantwo`.
`map`	A list containing the alternative genetic map. All chromosomes in `object` should have corresponding chromosomes in `map`, and markers must be in the same order in the two maps. There must be at least two markers on each chromosome in `map` that appear in `object`.

Details

The positions of pseudomarkers are determined by linear interpolation between markers. In the case of pseudomarkers beyond the ends of the terminal markers on chromosomes, we use the overall lengths of the chromosome in object and map to determine the new spacing.

Value

The input object with the positions of LOD scores revised to match those in the input map.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(hyper)

origmap <- pull.map(hyper)
newmap <- est.map(hyper)
hyper <- replacemap(hyper, newmap)
hyper <- calc.genoprob(hyper, step=0)
out <- scantwo(hyper, method="hk")
out.rev <- replacemap(out, origmap)

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