multloci: Summaries of multiple loci on a chromosome.

In fboehm/qtlbim: QTL Bayesian Interval Mapping

Description

Summaries and up to four plots showing loci found in MCMC samples for a chromosome.

Usage

qb.multloci(qbObject, chr = 1, cutoff = 25, nqtl, ...)
## S3 method for class 'qb.multloci'
plot(x, amount = 0.5, cex,
  split = TRUE, contour = TRUE, weight = TRUE, merge = TRUE, ...)
## S3 method for class 'qb.multloci'
summary(object, merge = TRUE, ...)

Arguments

qbObject	Object of class qb.
x,object	Object of class qb.multloci.
chr	Identifier for one chromosome.
cutoff	Smallest posterior probability for nqtl (ignored if nqtl provided).
nqtl	Number of QTL on chromosome (inferred by default).
amount	Amount to jitter points.
cex	Character expansion of plot symbols.
split	Split plots into four panels on one page if TRUE. Otherwise plot each panel separately. The split may be a numeric vector with values 1:4 signifying which panels to show. See details.
contour	Contour plot overlaid on pairs if TRUE.
weight	Inversely weight loci in density plot by number of QTL if TRUE.
merge	Merge across number of QTL if TRUE. Otherwise, show separate summary or plot by number of QTL. See details.
...	Parameters to qb.mainmodes or to methods.

Details

Find multiple loci in MCMC samples for chromosome chr. The number of QTL, nqtl is inferred from the histogram as the largest number of QTL above the percent cutoff.

The generic plot command produces the following plots: (1) density plot of main QTL grouped by QTL; (2) histogram of number of QTL; (3) density plot of epistatic pairs; (4) scatter plot of pairs of QTL. The density plots are divided into nqtl groups. The scatter plot shows pairs of main loci below diagonal and epistatic pairs above using codes corresponding to the number of QTL per sample; note that 3 QTL have 3 pairs, 4 QTL have 6, etc., and that solitary QTL are displayed along the diagonal.

split and merge control the manner of plotting. Setting merge to FALSE yields only density plots for main loci conditioned on the number of QTL per sample. Setting split to FALSE or to numbers between 1 and 4 yields plots on separate pages.

Author(s)

Brian S. Yandell, [e-mail]

References

http://www.qtlbim.org

See Also

plot.qb, qb.scantwo, qb.mainmodes

Examples

data(qbExample)

temp <- qb.multloci(qbExample, 1)
summary(temp)
plot(temp)
plot(temp, merge = FALSE)
summary(temp, merge = FALSE)

fboehm/qtlbim documentation built on Feb. 16, 2021, 12:04 a.m.