epistasis: Density Plots for Models Showing Epistasis and GxE...

In byandell/qtlbim: QTL Bayesian Interval Mapping

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, [e-mail]

References

http://www.qtlbim.org

Examples

data(qbExample)

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

byandell/qtlbim documentation built on Dec. 19, 2021, 12:47 p.m.