plot_outbred: Plot LOD curves for outbred data

In qtl.outbred: Interface for Genotype Probabilities from Outbred Intercross

Description

Plot the LOD curve including the markers for a genome scan with the single-QTL model.

Usage

plot_outbred(model, old.data, dimension = '1D', chr = -1, gap = 25, ...)

Arguments

model	An object of class scanone, as output by scanone.
old.data	An object of class cross. See read.cross for details.
dimension	A string giving the dimension of the QTL scan to be plotted, and the current version allows '1D' or '2D'.
chr	Optional vector indicating the chromosomes to plot.
gap	Gap separating chromosomes (in cM).
...	Other arguments. See package qtl for details.

Details

This function allow the user to plot the results produced by scanone. The LOD scores for single or multiple chromosomes are plotted with the markers indicated.

See also plot.scanone for plotting the scan results but with the probabilities on the marker positions.

Value

None

Author(s)

Ronnie Nelson and Xia Shen

See Also

impo.prob, qtl.outbred-package, plot.scanone,

Examples

## Not run: 
# ----- impo.prob example
file <- paste(R.home(), '/library/qtl.outbred/example_data.csv', sep = '')
data <- read.cross('csv', file = file, genotypes = c('AA', 'AB', 'BB'))
outbred.data <- impo.prob(cross.data = data, stepsize = 5)

# ----- QTL scan using Haley-Knott regression and plotting
hk.model <- scanone(outbred.data, method = 'hk', pheno.col = 2) 
plot_outbred(hk.model, data)

## End(Not run)

qtl.outbred documentation built on May 2, 2019, 5:56 p.m.