scanTwo: Genome Scan for Epistasis

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

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.

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.