plot.qb.mainmodes {qtlbim}R Documentation

Summaries of QTL modes by chromosome.

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, yandell@stat.wisc.edu

References

http://www.qtlbim.org

See Also

qb.multloci, summary.qb.scanone

Examples

data(qbExample)

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

[Package qtlbim version 1.9.3 Index]