genoprob: Grid point and genotype probability computation method

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

This function is used to compute putative QTL positions and genotypic probabilities at these positions. The genotypic probabilities for missing marker genotypes are also computed.

Usage

qb.genoprob(cross, map.function, step = 2,
  tolerance = 1e-6, stepwidth = "variable", ...)

Arguments

cross	An object of class cross. See read.cross for details.
map.function	Indicates what map function to use when converting genetic distances to recombination fractions. See calc.genoprob.
step	Distance (in cM) between positions at which putative QTL positions and their genotype probabilities are calculated. However, specifying step = 0 would assume marker positions as putative QTL locations and genotypic probabilities would be calculated only for markers with missing genotype.
tolerance	Minimum separation of markers enforced by jittermap.
stepwidth	Type of stepwidth for calc.genoprob; "variable" works best with MCMC sampling.
...	Extra arguments to pass to calc.genoprob.

Value

qb.genoprob first ensures marker separation is at least tolerance, and then computes genotype probabilities at pseudomarkers spaced approximately step units apart using calc.genoprob. See calc.genoprob for value.

Author(s)

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

References

http://www.qtlbim.org

See Also

jittermap, calc.genoprob.

Examples

## calculate grids and genotypic probabilites
cross <- qb.genoprob(cross,map.func="haldane",step=2)

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