View source: R/calc_genoprob_error.R
calc_genoprob_error | R Documentation |
Conditional genotype probabilities are calculated for each marker position and each individual given a map.
calc_genoprob_error( input.map, step = 0, phase.config = "best", error = 0.01, th.prob = 0.95, restricted = TRUE, verbose = TRUE )
input.map |
An object of class |
step |
Maximum distance (in cM) between positions at which the genotype probabilities are calculated, though for step = 0, probabilities are calculated only at the marker locations. |
phase.config |
which phase configuration should be used. "best" (default) will choose the maximum likelihood configuration |
error |
the assumed global error rate (default = 0.01) |
th.prob |
the threshold for using global error or genotype probability distribution contained in the dataset (default = 0.95) |
restricted |
if |
verbose |
if |
An object of class 'mappoly.genoprob' which has two elements: a tridimensional array containing the probabilities of all possible genotypes for each individual in each marker position; and the marker sequence with it's recombination frequencies
Marcelo Mollinari, mmollin@ncsu.edu
Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378
probs.error <- calc_genoprob_error(input.map = solcap.err.map[[1]], error = 0.05, verbose = TRUE)
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