haplo.stats (version 1.9.7)

plot.seqhap: Plot a seqhap object

Description

Method to plot an object of class seqhap. The p-values at each locus are based on sequentially combined loci, and they are plotted to visualize the p-values when scanning each locus using seqhap methods. Plots -log10(p-value) on the y-axis vs. the loci over which it was computed on the x-axis.

Usage

# S3 method for seqhap
plot(x, pval="hap", single=TRUE,
minp=.Machine$double.eps, ...)

Value

Nothing is returned.

Arguments

x

The object returned from seqhap

pval

Character string for the choice of p-value to plot. Options are: "hap" (sequential haplotype asymptotic p-value), "hap.sim" (sequential haplotype simulated p-value), "sum" (sequential summary asymptotic p-value), and "sum.sim" (sequential summary simulated p-value).

single

Logical, indicating whether to plot p-values for single-locus association tests. If TRUE, the pointwise p-values from the single-locus will be plotted using a dotted line.

minp

Smallest "allowable" p-value; any p-value smaller will be set to log10(minp). The default is the value closest to zero that can be represented in Splus/R.

...

Dynamic parameter for the values of additional parameters for the plot method. Accept the ylim parameter for plot() and other parameters for lines(), points(), and axis(). Recommended values to make locus labels vertical on the x-axis: for R: las=2, cex.axis=1.2 for S+: srt=90, cex.axis=1.2, adj=1

Details

The x-axis has tick marks for all loci. The y-axis is the -log10() of the selected p-value. For the sequential result for each locus, a horizontal line at the height of -log10(p-value) is drawn across the loci combined. The start locus is indicated by a filled triangle and other loci combined with the start locus are indicated by an asterisk or circle.

If the permutation p-value is zero, for plotting purposes it is set to 1/(n.sim+1).

References

Yu Z, Schaid DJ. (2007) Sequential haplotype scan methods for association analysis. Genet Epidemiol, in print.

See Also

seqhap, print.seqhap

Examples

  if (FALSE) {
    data(seqhap.dat)
    mydata.y <- seqhap.dat[,1]
    mydata.x <- seqhap.dat[,-1]
    data(seqhap.pos)
    myobj <- seqhap(y=mydata.y, geno=mydata.x, pos=seqhap.pos$pos)
    plot(myobj)
  }