qtl: formMarkerCovar – R documentation

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qtl

formMarkerCovar

Create matrix of marker covariates for QTL analysis

Description

Pull out a matrix of genotypes or genotype probabilities to use markers as covariates in QTL analysis.

Usage

formMarkerCovar(cross, markers, method=c("prob", "imp", "argmax"), ...)

Arguments

`cross`	An object of class `cross`. See `read.cross` for details.
`markers`	A vector of character strings of marker or pseudomarker names. Pseudomarker names may be of the form `"5@21.5"` (for chr 5 at 21.5 cM), but then all names must be of this form.
`method`	If `method="prob"`, the genotype probabilities from `calc.genoprob` are used; otherwise we use `fill.geno` to impute missing data, with this method.
`...`	Passed to `fill.geno`, if necessary.

Value

A matrix containing genotype probabilities or genotype indicators, suitable for use as covariates in scanone.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(hyper)
hyper <- calc.genoprob(hyper, step=0)
peakMarker <- "D4Mit164"
X <- formMarkerCovar(hyper, peakMarker)

out <- scanone(hyper, addcovar=X)

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