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

data(qbExample)

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

[Package qtlbim version 1.9.3 Index]