qb.close {qtlbim}R Documentation

Measures closeness of genetic architectures to target.

Description

Boxplots and summaries of how close MCMC samples of genetic architectures are to target architecture.

Usage

qb.close(qbObject, target = NULL, epistasis = TRUE, signed = FALSE,
  score.type = c("sq.atten","attenuation","variance","recombination",
  "distance"), ...)
## S3 method for class 'qb.close':
plot(x, category = c("pattern", "nqtl"), xlab,
  cutoff, sort.pattern = c("percent","score"), ...)
## S3 method for class 'qb.close':
summary(object, cutoff, digits = 0,
  show = "score", ... )

Arguments

qbObject Object of class qb.
x,object Object of class qb.close.
target Target architure as data frame with columns chrom and locus. Extracted from summary if target is a qb.scanone object. If target = NULL, score.type is set to "variance" to be compared with null model.
epistasis Include epistasis in patterns if TRUE.
signed Sign score. Most useful to examine single chromosome.
score.type Type of score to use as distance.
category Boxplots indexed by nqtl or pattern.
xlab Label for X axis (default taken from x object).
cutoff Percent cutoff for pattern inclusion in model selection. Default is 0.25 (0.5) if epistasis is TRUE (FALSE).
sort.pattern If type = "pattern", sort by percent posterior or by median of score.
digits Number of digits displayed for locus.
show Character string with name from object to show.
... Parameters to methods.

Details

Closeness for each loci is measured as 1-2r, with r the recombination rate. Thus unlinked loci have measure 0. Loci between a MCMC sample architecture and the target architecture on the same chromosome are matched by closest distance in cM between subsets of the the same length (if target has 2 QTL on chr 3 and sample has 3, consider all pairs from sample to find closest pair in 2-D). Measure per sample is sum across all loci. A quick way to generate a target is to use qb.BestPattern.

The score.type is "recombination" = r, the recombination rate; "attenuation" = 1-2r; "sq.atten" = squared attenuation, "distance" in cM, or genetic "variance".

Author(s)

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

References

http://www.qtlbim.org

See Also

qb.BestPattern, qb.hpdone

Examples

data(qbExample)

## Here target is known for simulated data.
target <- data.frame(chrom = c(1,1,2,3),
  locus = c(15,45,12,15))
temp <- qb.close(qbExample, target)
summary(temp)
plot(temp)
plot(temp, category = "nqtl")

## Or use target from qb.BestPattern
target <- summary(qb.BestPattern(qbExample))$best
qb.close(qbExample, target)

[Package qtlbim version 1.9.3 Index]