qb.BayesFactor {qtlbim} | R Documentation |
Model-averaged posteriors and Bayes factors computed for number and pattern of QTL, chromosomes and pairs of chromosomes showing epistasis.
qb.bf(...) qb.BayesFactor(qbObject, items = c("nqtl","pattern","chrom","pairs"), cutoff.pattern, cutoff.pairs = 1, nmax = 15, epistasis = TRUE, ...) ## S3 method for class 'qb.BayesFactor': plot(x, ...) ## S3 method for class 'qb.BayesFactor': summary(object, sort = TRUE, digits = 3, ...) ## S3 method for class 'qb.BayesFactor': print(x, ...)
qbObject |
An object of class qb . |
object |
Object of class qb.BayesFactor . |
x |
Object of class qb.BayesFactor . |
items |
Items to include in model selection assessment. These are
nqtl = Number of QTLs;
pattern = Pattern of QTL across chromosomes as
comma-separated chromosome numbers and colon-separated chromosome pairs;
chrom = Chromosome;
pairs = Epistatic pairs of chromosomes. |
cutoff.pattern |
Percent cutoff for pattern inclusion in model
selection. Default is 0.25 (0.5) if epistasis is TRUE
(FALSE ). |
cutoff.pairs |
Percent cutoff for epistatic pair inclusion in model selection. |
nmax |
Maximum number of model terms included per item (for
items "pattern" and "pairs" only). |
epistasis |
Include epistasis in patterns if TRUE . |
sort |
Sort by Bayes factor if TRUE . |
digits |
Number of significant digits for summary. |
... |
Additional arguments passed to generic plot, summary or print. |
qb.BayesFactor
(or qb.bf
for short) creates model
selection results for selected
items. These are based on marginal posteriors and priors, averaged
over all other model parameters. The posterior may be influenced by
prior, while Bayes factors are empirically less sensitive for QTL
model selection. The Bayes factors are computed relative to the
smallest term for each item, using the ratios of
posterior/prior
. Any pair of model terms can be compared as the
ratio of their Bayes factors.
List with items
, each containing:
posterior |
Posterior frequency of MCMC samples. |
prior |
Prior frequency. |
bf |
Rank-ordered Bayes factors relative to smallest value. |
bfse |
Approximate standard error for bf computed using binomial variance of MCMC samples. |
Brian S. Yandell, yandell@stat.wisc.edu
data(qbExample) temp <- qb.BayesFactor(qbExample) summary(temp) plot(temp)