qb.hpdone {qtlbim}R Documentation

Highest probability density (HPD) region.

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)

[Package qtlbim version 1.9.3 Index]