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)A matrix whose entry in the upper triangle is the log-likelihood test statistic for epistatic effect.
A numeric vector or a numeric matrix of one column (representing a phenotype for instance).
A data frame or matrix, representing covariates if not missing.
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.
An object from genoProb.
An object from estVC or aicVC, or an estimated variance-covariance matrix induced by relatedness and environment.
Whether to treat numeric coding of genotypes as numeric. If true, minorGenoFreq will be ignored.
Specify the minimum tolerable minor genotype frequency at a scanning locus if gdat is used.
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.
scanOne.