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
.