arch: Build genetic architecture with chromosomes, positions and...

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

These routines work in conjunction with qb.hpdone, qb.scantwo, qb.sliceone and step.fitqtl to infer the number, pattern and position of QTL from MCMC samples.

Usage

qb.arch(object, ...)
## Default S3 method:
qb.arch(object, chr, pos, tolerance = 10, ...)
## S3 method for class 'step.fitqtl'
qb.arch(object, main, epistasis, ...)
## S3 method for class 'qb.BestPattern'
qb.arch(object, ...)
## S3 method for class 'qb.arch'
summary(object, ...)
## S3 method for class 'qb.arch'
print(x, ...)

Arguments

object	Object for appropriate method: summary of object of class qb.scantwo for default; object of class step.fitqtl.
x	Object of class qb.arch.
chr	Vector of chromosome numbers.
pos	Vector of positions on chromosomes (much be same length as chr).
tolerance	Minimum distance for two QTL to be considered distinct.
main	Vector of chromosome identifiers with only main effects.
epistasis	Data frame with a 2-element vector of chromosome identifiers for each epistatic pair.
...	Not used here.

Details

Extract architecture in terms of chromosomes and positions of main QTL and identifiers of epistatic pairs of QTL. The step.fitqtl approach is used to compare an automatic fit to a user-defined set of main chromosomes and epistatic pairs.

Value

qtl	Data frame with main QTL as chr and pos.
by.num	Data frame with epistatic pairs indexed by chromosome number, labeled qtla and qtlb.
by.chr	List with elements chr and pos showing epistatic pairs. These elements are data frames with chromosomes and positions for each epistatic pair: rows are QTL number, columns are qtla and qtlb.
by.set	List of connected sets of epistatic chromosomes.

Author(s)

Brian S. Yandell

References

http://www.qtlbim.org

See Also

step.fitqtl, qb.sweave, qb.best

Examples

data(qbExample)

## Run qb.scantwo and get summary to use in qb.arch
temp <- summary(qb.scantwo(qbExample, type = "2logBF"),
  threshold = c(upper = 10))
## qb.arch default use. 
cross.arch <- qb.arch(temp, chr = c(1,1,2,3), pos = c(15,45,12,15))
cross.arch

byandell/qtlbim documentation built on Dec. 19, 2021, 12:47 p.m.