estimateRFSingleDesign: Estimate pairwise recombination fractions

In rohan-shah/mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Estimate pairwise recombination fractions, similar to estimateRF, but with different performance requirements in terms of compute time and storage.

Usage

estimateRFSingleDesign(
  object,
  recombValues,
  lineWeights,
  keepLod = FALSE,
  keepLkhd = FALSE,
  verbose = FALSE,
  markerRows = 1:nMarkers(object),
  markerColumns = 1:nMarkers(object)
)

Arguments

object	An object of class mpcross.
recombValues	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).
lineWeights	Values to use to correct for segregation distortion. This parameter should in general be left unspecified.
keepLod	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.
keepLkhd	Set to TRUE to compute the maximum value of the likelihood. Due to memory constraints this should generally be left as FALSE.
verbose	Output diagnostic information, such as the amount of memory required, and the progress of the computation.
markerRows	Used to estimate only a subset of the full matrix of pairwise recombination fractions.
markerColumns	Used to estimate only a subset of the full matrix of pairwise recombination fractions.

Details

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.

Value

An object of class mpcrossRF, which contains the original genetic data, and also estimated recombination fraction data.

rohan-shah/mpMap2 documentation built on July 21, 2020, 8:58 p.m.