quickEst: Very quick estimation of genetic map distances.

In ASMap: Linkage Map Construction using the MSTmap Algorithm

Very quick estimation of genetic map distances.

Description

Very quick estimation of genetic map distances for a constructed R/qtl object

Usage

quickEst(object, chr, map.function = "kosambi", ...)

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.

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.

Value

The cross object is returned with identical class structure as the inputted cross object.

Author(s)

Julian Taylor

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

See Also

est.map

Examples

data(mapDH, package = "ASMap")

mapDH1 <- quickEst(mapDH, map.function = "kosambi")

ASMap documentation built on Nov. 1, 2024, 9:08 a.m.