qb.varcomp {qtlbim} | R Documentation

## Variance components for Bayesian multiple QTL

### Description

These routines extract and summarize variance components for Bayesian multiple QTL. Variance components are averaged over genome loci. Covariates and GxE may be included.

### Usage

    qb.varcomp(qbObject, scan, aggregate = TRUE)
    ## S3 method for class 'qb.varcomp':
    summary(object, ...)
    ## S3 method for class 'qb.varcomp':
    print(x, ...)
    ## S3 method for class 'qb.varcomp':
    plot(x, log = TRUE, percent = 5, cex, ...)

### Arguments

`qbObject` | Object of class `qb`.
`object` | Object of class `qb.varcomp`.
`x` | Object of class `qb.varcomp`.
`scan` | Aggregated terms to include in created object (see below).
`aggregate` | Sum over individual components of aggregated terms if `TRUE`.
`log` | Use log10 of variances in plot if `TRUE`.
`percent` | Percentile between 0 and 100 for summaries.
`cex` | Character expansion for plot symbols. Default shrinks with number of MCMC iterations.
`...` | Arguments to pass along.

### Details

Variance components are organized as "main" ("add" and "dom"), "epistasis" ("aa", etc.), "fixcov" (for all fixed covariate terms), "rancov" (random covariates), and "GxE" (genotype by environment, including additive and dominance terms). Any subset of these may be chosen.

### Value

`qb.varcomp` creates a matrix with columns of samples for the variance components. Each row represents an MCMC iteration. Values are averaged over loci.

### Author(s)

Brian S. Yandell

### References

http://www.qtlbim.org

### See Also

`qb.mcmc`

### Examples

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

[Package qtlbim version 1.6.5 Index]