The cross object is returned with identical class structure as the
inputted cross object.
Arguments
object
An R/qtl object object with any class structure.
chr
A character string of linkage group names that require (re)estimation of
their genetic map distances.
map.function
Character string of either "koasmbi", "haldane",
"morgan" or "cf" defining the mapping
function to be used.
...
Other arguments passed to argmax.geno.
Author
Julian Taylor
Details
For linkage groups with large numbers of markers, the Hidden Markov algorithm in est.map
can be extremely slow. The computational burden for this algorithm
increases as the number of missing values and genotyping errors
increase. quickEst circumvents this by using the Viterbi
algorithm computationally implemented in argmax.geno of the
qtl package. Initial conservative estimates of the map distances
are calculated from inverting recombination fractions outputted from
est.rf. These are then passed to argmax.geno and
imputation of missing allele scores is performed along with
re-estimation of map distances.
References
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic
Linkage Map Construction and Diagnosis. Journal of Statistical Software,
79(6), 1--29.