R: Plot a haplo.score.slide Object

plot.haplo.score.slide {haplo.stats} | R Documentation

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

### 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.

### Value

Nothing is returned.

### 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)

[Package haplo.stats version 1.7.9 Index]