Plot the blups or interval outlier statistics from specififed iteratons of wgaim

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Description

Plots the interval blups/outlier statistics for specified iterations of wgaim. The interval blups/outlier statistics appear as a trace across the genome separated by chromosome and appropriately spaced by their distances.

Usage

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out.stat(object, intervalObj, int = TRUE, iter = NULL, chr = NULL, stat
= "os", ...)

Arguments

object

object of class "wgaim"

intervalObj

object of class "cross" or "interval"

int

logical value, if TRUE then plot interval outlier statistics. If FALSE then plot chromosome outlier statistics.

iter

numeric value determining which iterations will be plotted

chr

character vector naming the subset of chromosomes to plot. This can only be used when int is TRUE

stat

character string naming the value to be plotted. Default is "os" (outlier statistics). Other option is "blups" for the scaled empirical blups calculated during each iteration

...

arguments passed to "xyplot" or "barchart" (with some restrictions, see Details)

Details

By default the interval blups/outlier statistics are plotted in separate panels for each iteration in a set layout of 5 rows and one column. This cannot be adjusted and users should not attempt to use the layout argument. Viewing multiple pages can be done by specifying the appropriate iterations using the iter argument.

The set of QTL are obtained from the model and printed on the plot in their appropriate positions in each panel.

Value

The blups/outlier statistics are plotted in a trellis panel plot.

Author(s)

Julian Taylor

References

Julian Taylor, Arunas Vebyla (2011). R Package wgaim: QTL Analysis in Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.

See Also

tr.wgaim, wgaim

Examples

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## Not run: 
# fit wgaim model

rkyld.qtl <- wgaim(rkyld.asf, phenoData = phenoRxK, intervalObj = genoRxK,
merge.by = "Genotype", trace = "trace.txt", na.method.X = "include")

# plot QTL interval outlier statistics

out.stat(rkyld.qtl, genoRxK, iter = 1:5, cex = 0.4)


## End(Not run)