quickEst {ASMap} | R Documentation |
Very quick estimation of genetic map distances for a constructed R/qtl object
quickEst(object, chr, map.function = "kosambi", ...)
object |
An R/qtl |
chr |
A character string of linkage group names that require (re)estimation of their genetic map distances. |
map.function |
Character string of either |
... |
Other arguments passed to |
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.
The cross object is returned with identical class structure as the inputted cross object.
Julian Taylor
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.
data(mapDH, package = "ASMap")
mapDH1 <- quickEst(mapDH, map.function = "kosambi")