qb.BestPattern {qtlbim}R Documentation

Proximity of common genetic architecture patterns.

Description

Multidimensional scaling and hierarchical clustering of most common patterns of genetic architecture.

Usage

qb.best(...)
qb.BestPattern(qbObject, epistasis = TRUE,
  category = c("pattern", "nqtl"), cutoff, score.type =
  c("sq.atten","attenuation","variance","recombination","distance"),
  include = c("nested","all","exact"),
  center = c("median","mean"), level = 5, ...)
## S3 method for class 'qb.BestPattern':
plot(x, type = c("mds", "hclust"),
  main, xlab, method = "complete", cluster = 3, cexmax = 5,
  colmax = 75, cex, col,
  symbol = c("pattern","nqtl","cluster","c@n","c@p","n@p","c@n@p"), ...)
## S3 method for class 'qb.BestPattern':
summary(object, method = "complete", 
  cluster = 3, n.best = 1, ...)

Arguments

qbObject Object of class qb.
x,object Object of class qb.BestPattern.
epistasis Include epistasis in patterns if TRUE.
category Distances indexed by nqtl or pattern.
cutoff Percent cutoff for pattern inclusion in model selection. Default is 0.25 (0.5) if epistasis is TRUE (FALSE).
score.type Type of score to use as distance. See qb.close.
type Plot dendrogram for hclust or 2-D multidimensional scaling projection for mds.
main Main plot title as character string.
xlab Character string for horizontal (x) axis.
method Method for hierarchical clustering.
cluster Number of clusters desired.
n.best Number of better models to display.
cexmax Maximum font size (minimum is set to 1); patterns are displayed in mds plot proportional to their posterior probability.
colmax Maximum number of colors.
cex Manual override of font size for mds plot; should be length 1 or the number of patterns exceeding cutoff.
col Colors for plotting.
symbol Plot symbol for mds plot. Shorthand using at sign @ signifies catenation of two or more symbols into one.
include Action for model averaging of chromosome-specific locus and explained variance: use all MCMC samples that match the chromosome; use only MCMC samples for patterns that have the target pattern nested within them; or use only MCMC samples with the exact same target pattern.
center Method of estimating the center for locus and explained variance.
level Confidence level as percent between 0 and 100 for loci and variance contributions.
... Parameters to methods.

Details

This uses the closeness measure from qb.close to compute a similarity matrix among patterns whose posterior probabilities exceed cutoff. Distance = 1 - similarity is used for hierarchical clustering or multidimensional scaling.

The best pattern is chosen as the one with highest posterior mean; all other patterns are compared to that pattern in terms of the score.type. This best pattern is a natural target for qb.close.

Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

References

http://www.qtlbim.org

See Also

qb.close

Examples

data(qbExample)

temp <- qb.BestPattern(qbExample)
summary(temp, n.best = 3)
plot(temp, type = "hclust")
plot(temp)
plot(temp, symbol = "c@n")

best <- summary(temp)$best
temp <- qb.close(qbExample, best)
summary(temp)
plot(temp)

[Package qtlbim version 1.9.3 Index]