qb.arch {qtlbim} | R Documentation

## Build genetic architecture with chromosomes, positions and epistatic pairs.

### 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.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`

### Examples

    ## 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

[Package qtlbim version 1.6.5 Index]