plot.qb.loci {qtlbim} | R Documentation |
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.
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, ...)
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 . |
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.
Brian S. Yandell, yandell@stat.wisc.edu
data(qbExample) temp <- qb.loci(qbExample) plot(temp) summary(temp) temp <- qb.loci(qbExample, "all") plot(temp) summary(temp)