QTLRel: scanTwo – R documentation

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scanTwo

Genome Scan for Epistasis

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

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

`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.

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