qb.model {qtlbim} | R Documentation |
This function sets up a genome-wide interacting QTL model by specifying global constraints on models and priors on unknowns.
qb.model(cross, epistasis = TRUE, main.nqtl = 3, mean.nqtl = main.nqtl + 3, max.nqtl = NULL, interval = NULL, chr.nqtl = NULL,intcov = c(0), depen = FALSE, prop = c(0.5, 0.1, 0.05), ...)
cross |
An object of class cross . See read.cross for details. |
epistasis |
indicates if epistasis is included in the model: TRUE or FALSE |
main.nqtl |
prior expected number of main effect QTLs. |
mean.nqtl |
prior expected number for all QTLs on all chromosomes including QTLs with main effects, epistatic effects and gene-environment interactions. |
max.nqtl |
maximum number of QTLs allowed in the model. Default
is l+3sqrt{l} where l is main.qtl for
non-epistatic model and mean.qtl for epistatic model. |
interval |
minimum distance between any two flanking QTLs for all chromosomes. Default is the average distance between markers in each chromosome. |
chr.nqtl |
list of the maximum number of QTLs allowed to be detected
on each chromosome. Default is the length of the chromosome
divided by interval . |
intcov |
list of the fixed covariates with which gene-environment interaction will be considered. |
depen |
=TRUE will use dependent prior for indicator variables of epistatic effects. |
prop |
prior inclusion probabilities for epistatic effects in three different scenarios:
when none,one and both the main effects of the two interacting QTL are
included in the model. Note that the sum of the probabilities need not
be equal to 1 and prop should be specified only when depen=TRUE .
|
... |
Not used. |
This function defines the model for Bayesian QTL mapping using qb.mcmc
.
This model considers two-way interaction as the highest level of both gene-gene and
gene-environment interactions.
qtl_envi |
Indicates if there is an interaction between the QTLs and environmental variables: TRUE or FALSE. |
This function returns a list and hence should have a differenct name from
that of the cross
object.
Dr. Nengjun Yi, et al., nyi@ms.ssg.uab.edu
qbModel <- qb.model(cross, chr.nqtl = rep(3,nchr(cross)), prop = c(0.5, 1, 0.5), intcov = 1)