plot.family.lods: Plot family contribution to peak LOD

In multic: Quantitative Linkage Analysis Tools using the Variance Components Approach

Description

Plot the top N families that contribute to the peak LOD score as obtained from a multic object

Usage

plotFamilyLods(x, npeakfams=5, title=NULL, title.cex=0.75, legend=T,
               legend.loc=c("left", "middle", "right", "extra"),
               type=c("top", "total", "proportion", "all"), ...)

Arguments

x	a multic object
npeakfams	number of top families to plot
title	title for the plot
title.cex	character size for the title
legend	logical (default = TRUE) indicating whether a legend is displayed or not
legend.loc	character string indicating the general legend location, if legend =T. "left" indicates the top left, "right" indicates the top right, "middle" indicates the upper middle, and "extra" indicates the legend should go on a separate plot.
type	character string indicating which plot should be shown. "top" shows the top npeakfams families, "total" shows the top families plus the overall total, "proportion" shows the percentage for the top families of the total LOD score, and "all" shows all 3 plots.
...	additional parameters to alter the default behavior of the plot.

Details

Based on the peak total lod score for the multic object, determine which families contribute most to that peak. Then display their contribution across the entire area that was used to fit the multic object.

Value

the lod scores for the top families

Note

The multic object must have been fit with the option "calc.fam.log.liks=TRUE". Additionally, the function will not work on polygenic multic objects.

See Also

multic.object, multic

Examples

## Not run: 
mult10 <- multic(sys.avg ~ sex + agexam + agexam^2, data=d10,
                 famid=famid, id=id, dadid=fa, momid=mo, sex=sex,
                 mloci='multicInput/mloci.out.gz', share='multicInput/share.out.gz',
                 calc.fam.log.liks=T)

plotFamilyLods(mult10, npeakfams=3, plot="total")

## End(Not run)

multic documentation built on Jan. 15, 2017, 9:30 a.m.