R: Genome Scan for Epistasis

scanTwo {QTLRel} | R Documentation

## Genome Scan for Epistasis

### Description

Evaluate log-likelihood ratio test statistic for epistasis (QTL by QTL interaction).

### Usage

    scanTwo(y, x, gdat, prdat = NULL, vc = NULL, numGeno = FALSE,
       minorGenoFreq = 0, rmv = TRUE)

### Arguments

`y` | A numeric vector or a numeric matrix of one column (representing a phenotype for instance).
`x` | A data frame or matrix, representing covariates if not missing.
`gdat` | Genotype data. Should be a matrix or a data frame, with each row representing an observation and each column a marker locus. The column names should be marker names. Optional if an object `prdat` from `genoProb` is used as an argument.
`prdat` | An object from `genoProb`.
`vc` | An object from `estVC` or `aicVC`, or an estimated variance-covariance matrix induced by relatedness and environment.
`numGeno` | Whether to treat numeric coding of genotypes as numeric. If true, `minorGenoFreq` will be ignored.
`minorGenoFreq` | Specify the minimum tolerable minor genotype frequency at a scanning locus if `gdat` is used.
`rmv` | A logical variable. If true, then the scanning locus will be skipped if the minor genotype frequency at the locus is smaller than `minorGenoFreq`. Otherwise, the scanning process will stop and return with NULL.

### Value

A matrix whose entry in the upper triangle is the log-likelihood test statistic for epistatic effect.

### See Also

`scanOne`.

[Package QTLRel version 1.0 Index]