qtl: plot.rfmatrix – R documentation

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plot.rfmatrix

Plot recombination fractions or LOD scores for a single marker

Description

Plot a slice (corresponding to a single marker) through the pairwise recombination fractions or LOD scores calculated by est.rf and extracted with pull.rf.

Usage

## S3 method for class 'rfmatrix'
plot(x, marker, ...)

Arguments

`x`	An object of class `rfmatrix`, as output by `pull.rf`.
`marker`	A single marker name, as a character string.
`...`	Optional arguments passed to `plot.scanone`.

Value

An object of class "scanone" (as output by scanone, and which may be summarized by summary.scanone or plotted with plot.scanone), containing the estimated recombination fractions or LOD scores for the input marker against all others.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(fake.f2)

fake.f2 <- est.rf(fake.f2)
marker <- markernames(fake.f2, chr=5)[6]
lod <- pull.rf(fake.f2, "lod")
plot(lod, marker, bandcol="gray70")

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