loci: Jittered plot of Bayesian QTL loci samples by chromosome

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

Each point is one locus from the Bayesian QTL estimates, plotted vertically by chromosome, jittered to give a sense of density. Separate colored vertical bands by loci element.

Usage

qb.loci(qbObject, loci = c("main", "epistasis", "GxE"), covar, ...)
## S3 method for class 'qb.loci'
plot(x, loci, labels = FALSE, amount = 0.35, cex, col, ...)
## S3 method for class 'qb.loci'
print(x, ...)
## S3 method for class 'qb.loci'
summary(object, digit = 1, ...)

Arguments

qbObject	Object of class qb.
loci	Character string identifying MCMC sample elements; may include "main", "epistasis", "GxE" and "all".
covar	Fixed covariate(s) for "GxE" loci; default is all fixed covariates involved in GxE interactions.
x	Object of class qb.loci.
object	Object of class qb.loci.
labels	Include marker labels if TRUE.
amount	Amount of jitter (between 0 and .45)
cex	Character expansion (may be invisible if too small–default based on number of MCMC samples).
col	Character string with colors named by loci; also includes color for marker lines.
digit	Number of digits for roundoff of loci quantiles.
...	Graphical parameters can be given as arguments to plot. Not used in qb.loci.

Details

Focuses attention on chromosome lengths and concentration of QTL loci estimates. Horizontal lines at markers. Separate bands by loci for each chromosome. Adjust amount and cex to modify look of plot. Most useful when looking at multiple chromosomes.

Author(s)

Brian S. Yandell, [e-mail]

References

http://www.qtlbim.org

See Also

jitter,subset.qb

Examples

data(qbExample)

temp <- qb.loci(qbExample)
plot(temp)
summary(temp)
temp <- qb.loci(qbExample, "all")
plot(temp)
summary(temp)

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