haplo.stats (version 1.9.7)

plot.haplo.score.slide: Plot a haplo.score.slide Object

Description

Method function to plot an object of class haplo.score.slide. The p-values from haplo.score.slide are for sub-haplotypes of a larger chromosomal region, and these are plotted to visualize the change in p-values as the sub-haplotype "slides" over a chromosome. Plot -log10(p-value) on the y-axis vs. the loci over which it was computed on the x-axis.

Usage

# S3 method for haplo.score.slide
plot(x, pval="global", dist.vec=1:x$n.loci, ...)

Value

Nothing is returned.

Arguments

x

The object returned from haplo.score.slide

pval

Character string for the choice of p-value to plot. Options are: "global" (the global score statistic p-value based on an asymptotic chi-square distribution), "global.sim" (the global score statistic simulated p-value), and "max.sim" (the simulated p-value for the maximum score statistic).

dist.vec

Numeric vector for position (i.e., in cM) of the loci along a chromosome. Distances on x-axis will correspond to these positions.

...

Dynamic parameter for the values of additional parameters for the plot method. Some useful options for manageing the x-axis labels are cex.axis, las, and srt.

Details

The x-axis has tick marks for all loci. The y-axis is the -log10() of the selected p-value. For each haplo.score result, plot a horizontal line at the height of -log10(p-value) drawn across the loci over which it was calculated. Therefore a p-value of 0.001 for the first 3 loci will plot as a horizontal line plotted at y=3 covering the first three tick marks. If the p-value for a set of loci is zero or very near zero, it is set to a minimum. Global asymptotic p-values of zero are set to the minimum of an epsilon or the lowest non-zero p-value in the region. Simulated p-values equal to zero are set to 0.5 divided by the total number of simulations performed.

References

Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. "Score tests for association of traits with haplotypes when linkage phase is ambiguous." Amer J Hum Genet. 70 (2002): 425-434.

See Also

haplo.score.slide

Examples

# This example has a long run-time, therefore it is commented

#   data(hla.demo)
#   attach(hla.demo)
#   geno.11 <- hla.demo[,-c(1:4)]
#   label.11 <- c("DPB","DPA","DMA","DMB","TAP1","TAP2","DQB","DQA","DRB","B","A")

#For an ordinal trait, slide by 3 loci, and simulate p-values:
#   y.ord <- as.numeric(resp.cat)
#   slide.ord.sim <-  haplo.score.slide(y.ord, geno.11, trait.type = "ordinal",
#                              n.slide=3, locus.label=label.11, simulate=TRUE,
#                              sim.control=score.sim.control(min.sim=500))

#   print(slide.ord.sim)
#   plot(slide.ord.sim)
#   plot(slide.ord.sim, pval="global.sim", las=2, cex.axis=.8)
#   plot(slide.ord.sim, pval="max.sim", srt=90, cex.axis=.8)