plot.qb.epistasis {qtlbim} | R Documentation

## Density Plots for Models Showing Epistasis and GxE Interactions.

### Description

Produces density plots of models showing epsistasis (`qb.epistasis`) or GxE interactions (`qb.intcov`). The vertical axis shows magnitude of effect, horizontal axis shows chromosomes in epistatic pairs or covariate by chromosome. Paralell plots are produced for each of the entries in the `effects` parameter.

### Usage

    qb.epistasis(qbObject, effects = c("aa", "ad", "da", "dd"),
      cutoff = 1, maxpair = 5, pairs, ...)
    qb.intcov(qbObject, covar, effects = c("add","dom"),
      cutoff = 1, nmax = 5, cov.chr, ...)
    ## S3 method for class 'qb.epistasis':
    plot(x, effects, cex = 0.5, main, ... )
    ## S3 method for class 'qb.epistasis':
    print(x, ... )
    ## S3 method for class 'qb.epistasis':
    summary(object, ... )

### Arguments

`qbObject` | An object of class `qb`.
`object` | Object of class `qb.epistasis`.
`x` | Object of class `qb.epistasis`.
`cutoff` | The `cutoff` parameter for number of epistatic pairs.
`maxpair` | Maximum number of epistatic pairs shown.
`pairs` | A character vector of chromosome pairs to examing for epistatic pairs. Chromosome names are separated by a dot.
`covar` | Covariate(s) to include; default is `seq(nfixcov)` where `nfixcov` is taken from `qb.data`.
`nmax` | Maximum number of covariate chromosomes shown.
`cov.chr` | A character vector of covariate by chromosome pairs to examing for GxE effects. Covariate names and chromosome names are separated by a dot.
`effects` | Character string of model effects.
`cex` | Horizontal expansion factor for characters in the plot. See `par`.
`main` | Main titles for plots; default is `effects`.
`...` | Arguments passed to generic `plot`.

### Value

Returns a table of counts of epistatic pairs with counts above the cutoff value.

### Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

### References

http://www.qtlbim.org

### Examples

    temp <- qb.epistasis(qbExample)
    summary(temp)
    plot(temp)
    temp <- qb.intcov(qbExample)
    summary(temp)
    plot(temp)

[Package qtlbim version 1.6.5 Index]