plot.haplo.score: Plot Haplotype Frequencies versus Haplotype Score Statistics

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Plot Haplotype Frequencies versus Haplotype Score Statistics

Description

Method function to plot a class of type haplo.score

Usage

## S3 method for class 'haplo.score'
plot(x, ...)

Arguments

x	The object returned from haplo.score (which has class haplo.score).
...	Dynamic parameter for the values of additional parameters for the plot method.

Details

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.

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

Examples

  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)

haplo.stats documentation built on Jan. 22, 2023, 1:40 a.m.