hpd: Highest probability density (HPD) region.

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

Determine HPD region across genome, including position of posterior mode.

Usage

qb.hpdone(qbObject, level = 0.5, profile = "2logBF",
  effects = "cellmean", scan = "sum", chr, smooth = 3, ...)
## S3 method for class 'qb.hpdone'
summary(object, chr, digits = 3, ...)
## S3 method for class 'qb.hpdone'
print(x, ...)
## S3 method for class 'qb.hpdone'
plot(x, chr, ...)

Arguments

qbObject	Object of class qb.
object	Object of class qb.hpdone.
x	Object of class qb.hpdone.
level	Value between 0 and 1 of HPD coverage.
scan	Elements to scan; usually one of "sum", "mean", "epistasis", "GxE".
smooth	Degree of smoothing.
chr	Chromosomes to include; default determined by HPD region.
effects	Effects are "cellmean" for means by genotype; "estimate" for estimates of Cockerham main effects.
profile	Objective profile for plot; default is "2logBF"; other choices found in option type for qb.scanone.
digits	Number of digits for round.
...	Extra parameters passed along to plot.

Details

Determine 100*level percent HPD region. Subset chromosomes based on HPD region. Create genome scans for profile and effects.

Value

qb.hpdone is a list with a hpd.region summary matrix and qb.scanone objects for the profile and effects. A summary of a qb.hpdone object yields a matrix with columns for

chr	chromosome number
n.qtl	estimated number of QTL on chromosome
pos	estimated position of QTL
lo.nn%	lower nn% HPD limit
hi.nn%	upper nn% HPD limit
profile	Peak of profile, identifed by the profile type.
effects	Columns for the effects, appropriately labeled.

Author(s)

Brian S. Yandell

References

http://www.qtlbim.org

See Also

qb.scanone, qb.hpdchr

Examples

data(qbExample)

temp <- qb.hpdone(qbExample)
summary(temp)
plot(temp)

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