Plot LOD curves for outbred data

Description

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

Usage

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## S3 method for class 'outbred'
plot(x, old.data = data, chr = -1, gap = 25, ...)

Arguments

x

An object of class outbred, as output by outbred.

old.data

An object of class cross. See read.cross for details.

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

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## 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'))
path <- paste(R.home(), '/library/qtl.outbred/', sep = '')
outbred.data <- impo.prob(cross.data = data, path = path, stepsize = 5)

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

## End(Not run)