mpMap2 (version 1.0.4)

combineKeepRF: Combine mpcross objects, keeping recombination fraction data

Description

Combine mpcross objects, keeping recombination fraction data

Usage

combineKeepRF(
  object1,
  object2,
  verbose = TRUE,
  gbLimit = -1,
  callEstimateRF = TRUE,
  skipValidity = FALSE
)

Arguments

object1

An object of class mpcrossRF

object2

Another object of class mpcrossRF

verbose

Passed straight through to estimateRF

gbLimit

Passed straight through to estimateRF

callEstimateRF

Should estimateRF be called, to compute any missing estimates?

skipValidity

Should we skip the validity check for object construction, in this function? Running the validity checks can be expensive, and in theory internal package code is trusted to generate valid objects.

Value

A new object of class mpcrossRF containing the combined information of the two input objects.

Details

This function takes two objects containing disjoint sets of markers, each containing estimated recombination fractions for their individual sets of markers. A new object is returned that contains the combined set of markers, and also contains recombination fraction data.

This function is more efficient than other ways of achieving this, as it keeps the recombination fraction data contained in the original objects. If callEstimateRF is TRUE, it also computes the missing recombination fraction estimates between markers in different objects, using a call to estimateRF.