Estimate pairwise recombination fractions, similar to estimateRF, but with different performance requirements in terms of compute time and storage.
estimateRFSingleDesign(
object,
recombValues,
lineWeights,
keepLod = FALSE,
keepLkhd = FALSE,
verbose = FALSE,
markerRows = 1:nMarkers(object),
markerColumns = 1:nMarkers(object)
)An object of class mpcross.
a vector of test values to use for the numeric maximum likelihood step. Must contain 0 and 0.5, and must have less than 255 values in total. The default value is c(0:20/200, 11:50/100).
Values to use to correct for segregation distortion. This parameter should in general be left unspecified.
Set to TRUE to compute the likelihood ratio score statistics for testing whether the estimate is different from 0.5. Due to memory constraints this should generally be left as FALSE.
Set to TRUE to compute the maximum value of the likelihood. Due to memory constraints this should generally be left as FALSE.
Output diagnostic information, such as the amount of memory required, and the progress of the computation.
Used to estimate only a subset of the full matrix of pairwise recombination fractions.
Used to estimate only a subset of the full matrix of pairwise recombination fractions.
An object of class mpcrossRF, which contains the original genetic data, and also estimated recombination fraction data.
Estimate pairwise recombination fractions, similar to estimateRF, but with different performance requirements in terms of compute time and storage. Specifically, this version is expected to perform better when there is only a single population.