plot.seqhap {haplo.stats} | R Documentation |
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.
## S3 method for class 'seqhap': plot(x, pval="hap", single=TRUE, ...)
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. |
... |
Dynamic parameter for the values of additional parameters for the plot method. Accept values that will apply to plot() 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 |
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 simulated p-value for a set of loci is zero, it is set to .5 / n.sim.
Nothing is returned.
Yu Z, Schaid DJ. (2007) Sequential haplotype scan methods for association analysis. Genet Epidemiol, in print.
setupData(seqhap.dat) mydata.y <- seqhap.dat[,1] mydata.x <- seqhap.dat[,-1] setupData(seqhap.pos) myobj <- seqhap(y=mydata.y, geno=mydata.x, pos=seqhap.pos$pos, n.sim=100) plot(myobj)