qb.scantwo {qtlbim} | R Documentation

## Genome Scan for Pairs of Loci Involved in Phenotypic Trait

### Description

This method extracts iteration diagnostics and pair loci from the `qb` object and returns a data frame (of class `qb.scanone`) containing information on environmental variance, explained variance components, epistatic and non-epistatic variance components.

### Usage

    qb.scantwo(qbObject, epistasis = TRUE, scan, type,
      upper.scan = "epistasis", lower.scan = "full", covar,
      adjust.covar, chr, min.iter = 1, verbose = FALSE)

### Arguments

`qbObject` | An object of class `qb`.
`epistasis` | If `TRUE` information on epistasis is included in the return value.
`scan` | List of diagnostics to scan (see below).
`type` | Vector of two scan types; default is "heritability" (see below).
`upper.scan` | Vector of diagnostics to scan for upper triangle (see below).
`lower.scan` | Vector of diagnostics to scan for lower triangle (see below).
`covar` | Covariate(s) to include; default is `seq(nfixcov)` where `nfixcov` is taken from `qb.data`. Set to 0 to exclude any covariates.
`adjust.covar` | Adjustments to covariates. Default is `NA`, which adjusts by covariate mean values. Values are assumed to be in order of fixed covariates.
`chr` | Chromosomes to subset on if not `NULL`.
`min.iter` | Include only samples at loci if minimum number of iterations is at least `min.iter`; default is to include all (`min.iter` = 1).
`verbose` | Give verbose feedback if `TRUE`.

### Details

The `scan` and `type` are similar to those used in `qb.scanone`. However, here `scan` is a list and `type` is a vector, each with elements "lower" and "upper". You can either specify `scan` as a list, or profide `upper.scan` and `lower.scan` separately.

The `scan` defaults for types other than counts to `list(upper = "epistasis", lower = "full")`; you can modify the list `scan` or the separate options `upper.scan` and `lower.scan`. The string "epistasis" is short-hand for the epistatic effects, `c("aa", "ad", "da", "dd")`. The string "full" is shorthand for the epistatics effects plus main effects, `c("add", "dom")`, plus any GxE terms.

The `type` defaults to `c(upper = "LPD", lower = "LPD")`. See `qb.scanone` for the range of possible types. Mostly the 2-D version of `type` provides marginal summaries for pairs of loci. However, for type `"nqtl"`, the marginal summaries involving main effects (e.g. with `scan` values `"full"` or `"main"` or `"add"` or `"dom"`) show, for each pair of chromosomes, the average number of QTL at both chromosomes.

### Value

Returns an object of class `qb.scantwo` (a data frame) containing effects selected according to `type` and `scan`.

### Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

### References

http://www.qtlbim.org

### See Also

`plot.qb.scanone`

### Examples

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

[Package qtlbim version 1.6.5 Index]