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QTLRel (version 1.14)

scanTwo: 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)

Value

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

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.

See Also

scanOne.