qb.genoprob {qtlbim} | R Documentation |
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.
qb.genoprob(cross, map.function, step = 2, tolerance = 1e-6, stepwidth = "variable", ...)
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 . |
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.
Dr. Nengjun Yi, et al., nyi@ms.ssg.uab.edu
## calculate grids and genotypic probabilites cross <- qb.genoprob(cross,map.func="haldane",step=2)