haplo.stats (version 1.7.6)

plot.haplo.score: 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.

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.

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.

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)