- genoprobs
A matrix of genotype probabilities, individuals x genotypes.
If NULL, we create a single intercept column, matching the individual IDs in pheno.
- pheno
A numeric vector of phenotype values (just one phenotype, not a matrix of them)
- kinship
Optional kinship matrix.
- addcovar
An optional numeric matrix of additive covariates.
- nullcovar
An optional numeric matrix of additional additive
covariates that are used under the null hypothesis (of no QTL)
but not under the alternative (with a QTL). This is needed for
the X chromosome, where we might need sex as a additive
covariate under the null hypothesis, but we wouldn't want to
include it under the alternative as it would be collinear with
the QTL effects.
- intcovar
An optional numeric matrix of interactive covariates.
- weights
An optional numeric vector of positive weights for the
individuals. As with the other inputs, it must have names
for individual identifiers.
- contrasts
An optional numeric matrix of genotype contrasts, size
genotypes x genotypes. For an intercross, you might use
cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)) to get
mean, additive effect, and dominance effect. The default is the
identity matrix.
- model
Indicates whether to use a normal model (least
squares) or binary model (logistic regression) for the phenotype.
If model="binary", the phenotypes must have values in
\([0, 1]\).
- zerosum
If TRUE, force the genotype or allele coefficients
sum to 0 by subtracting their mean and add another column with
the mean. Ignored if contrasts is provided.
- se
If TRUE, calculate the standard errors.
- hsq
(Optional) residual heritability; used only if
kinship provided.
- reml
If kinship provided: if reml=TRUE, use
REML; otherwise maximum likelihood.
- blup
If TRUE, fit a model with QTL effects being random, as in scan1blup().
- ...
Additional control parameters; see Details;