modes: Summaries of QTL modes by chromosome.

In fboehm/qtlbim: QTL Bayesian Interval Mapping

Description

Determine number of QTL per chromosome and estimate peaks and valleys.

Usage

qb.split.chr(qbObject, split, ...)
qb.epimodes(qbObject, cutoff = 1, nqtl, n.iter, pairloci, ...)
qb.mainmodes(qbObject, cutoff = 25, nqtl, n.iter, mainloci, ...)
## S3 method for class 'qb.mainmodes'
summary(object, digits = 4, ...)

Arguments

qbObject	Object of class qb.
split	List of split locations; names of list must correspond to chromosome names in qbObject. Default set by call to qb.mainmodes with addition arguments in ....
object	Object of class qb.mainmodes.
cutoff	Cutoff for neglible number of QTL.
nqtl	Vector of number of QTL per chromosome.
n.iter	Number of iterations (for internal use only).
mainloci	Object containing mainloci data (for internal use only).
pairloci	Object containing pairloci data (for internal use only).
digits	Number of significant digits.
...	Parameters to qb.mainmodes or to methods.

Details

Cut off histogram of number of QTL per chromosome such that cumulative percent above number is less than cutoff. Once nqtl is determined or provided in call, divide MCMC samples using linear discriminant analysis (lda) and find peak locations per class. Use these peak locations to find locations of valleys between peaks. These valleys are used to divide MCMC samples into separate QTL for analysis. Currently this is used by summary.qb.scanone and qb.multloci.

qb.split.chr sets up a split for chromosomes for at valleys between inferred multiple QTL as an attribute of a returned qbObject. This is done by default when qbObject is created, and is stored as an attribute available as qb.get(qbObject, "split.chr").

Author(s)

Brian S. Yandell, [e-mail]

References

http://www.qtlbim.org

See Also

qb.multloci, summary.qb.scanone

Examples

data(qbExample)

temp <- qb.mainmodes(qbExample)
summary(temp)

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