Plot Haplotype Frequencies versus Haplotype Score Statistics
Method function to plot a class of type haplo.score
## S3 method for class 'haplo.score' plot(x, ...)
x |
The object returned from haplo.score (which has class haplo.score). |
... |
Dynamic parameter for the values of additional parameters for the plot method. |
This is a plot method function used to plot haplotype frequencies on the x-axis and haplotype-specific scores on the y-axis. Because haplo.score is a class, the generic plot function can be used, which in turn calls this plot.haplo.score function.
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.
haplo.score
data(hla.demo)
geno <- as.matrix(hla.demo[,c(17,18,21:24)])
keep <- !apply(is.na(geno) | geno==0, 1, any)
hla.demo <- hla.demo[keep,]
geno <- geno[keep,]
attach(hla.demo)
label <- c("DQB","DRB","B")
# For quantitative, normally distributed trait:
score.gaus <- haplo.score(resp, geno, locus.label=label,
trait.type = "gaussian")
plot.haplo.score(score.gaus)
## try: locator.haplo(1)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.