R: Plot Haplotype Frequencies versus Haplotype Score Statistics

plot.haplo.score {haplo.stats} | R Documentation

## 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)

[Package haplo.stats version 1.7.9 Index]