model: Set up interacting QTL model for qb.mcmc

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

This function sets up a genome-wide interacting QTL model by specifying global constraints on models and priors on unknowns.

Usage

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), contrast = TRUE, ...)	     
  

Arguments

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+3√{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	logical or 0/1 vector for fixed covariates indicating which gene-environment interaction will be considered (default is all FALSE, no GxE).
depen	=TRUE will use dependent prior for indicator variables of epistatic effects.
prop	prior inclusion probabilities for epistatic effects in three different scenarios: when both (default 0.5), one (0.1) or none (0.05) of 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.
contrast	Use Cockerham model if TRUE; otherwise estimate genotypic values.
...	Not used.

Details

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.

Value

qtl_envi

Indicates if there is an interaction between the QTLs and environmental variables: TRUE or FALSE.

Note

This function returns a list and hence should have a differenct name from that of the cross object.

Author(s)

Dr. Nengjun Yi, et al., [e-mail]

References

http://www.qtlbim.org

See Also

qb.data, qb.genoprob, qb.mcmc

Examples

qbModel <- qb.model(cross, chr.nqtl = rep(3, qtl::nchr(cross)), intcov = 1,
  interval = rep(10,3))  

byandell/qtlbim documentation built on Dec. 19, 2021, 12:47 p.m.