qtl: plot.scantwoperm – R documentation

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qtl

plot.scantwoperm

Plot permutation results for a 2d, 2-QTL genome scan

Description

Plot a histogram of the permutation results from a two-dimensional, two-QTL genome scan.

Usage

## S3 method for class 'scantwoperm'
plot(x, lodcolumn=1, include_rug=TRUE, ...)

Arguments

`x`	An object of class `"scantwoperm"`, as output by `scantwo` when `n.perm` is specified.
`lodcolumn`	This indicates the LOD score column to plot. This should be a single number between 1 and the number of LOD columns in the object input.
`include_rug`	If TRUE, include a call to `rug`.
`...`	Passed to the function `hist` when it is called.

Details

The function plots a histogram of the permutation results obtained by scantwo when n.perm is specified. Separate histograms are provided for the five LOD scores, full, fv1, int, add, and av1.

Value

None.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(fake.bc)
fake.bc <- calc.genoprob(fake.bc)

operm2 <- scantwo(fake.bc, method="hk", n.perm=10)
plot(operm2)

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