plot.qb.epistasis {qtlbim} | R Documentation |
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.
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, ... )
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 . |
Returns a table of counts of epistatic pairs with counts above the cutoff value.
Brian S. Yandell, yandell@stat.wisc.edu
data(qbExample) temp <- qb.epistasis(qbExample) summary(temp) plot(temp) temp <- qb.intcov(qbExample) summary(temp) plot(temp)