Re-estimate large gaps in a genetic map from IBD genotype imputations
estimateMapFromImputation(
mpcrossMapped,
gapSize = 5,
recombinationFractions = c(0:60/600, 11:49/100)
)An object of class mpcrossMapped
The size of the gap to reestimate.
The recombination fractions to use for numerical maximum likelihood estimation
An object of class mpcrossMapped with a re-estimated map.
For larger gaps in a genetic map, the pairwise recombination fractions are not (by themselves) useful. An alternative is to estimate the IBD genotypes, and use the imputed IBD genotypes to re-estimate larger gaps using numerical maximum likelihood. Although the IBD genotypes are based on an existing genetic map, they may not be strongly affected by a large gap that has been poorly estimated, as the imputed IBD genotypes represent a consensus across all nearby markers, and also allow for genotyping errors. As a result, the re-estimated map may be different from the original map, and potentially more accurate.