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, smooth = 3, ...)

### 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`

### Examples

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

[Package qtlbim version 1.6.5 Index]