plot.haplo.score.slide {haplo.stats} | R Documentation |
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.
plot.haplo.score.slide(x, pval="global", dist.vec=1:x$n.loci, cex=.8, srt=270, ...)
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. |
cex |
Character expansion size. |
srt |
String rotation in degrees measured counterclockwise from horizontal. Applies to x-axis (locus) labels. |
... |
Dynamic parameter for the values of additional parameters for the plot method. |
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.
Nothing is returned.
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.
#This example is run completely in the haplo.score.slide # setupData(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") # plot(slide.ord.sim, pval="max.sim")