mpcollapse: Collapse an mpcross object into a binned object

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Collapses an mpcross object into bins. Within bins, markers are grouped by founder distribution pattern and missing genotypes imputed. Haplotypes are formed for markers with unique FDPs and determine the bin alleles. Information on which markers belong to each bin is retained within the output object.

Usage

mpcollapse(object, method = c("rf", "cor"), adj = FALSE, cutoff = 0,
  consensusProbability = 0.75, missingCutoff = 0.25)

Arguments

object	Object of class mpcross
method	Choice of whether to bin based on recombination fraction or correlation
adj	Flag for whether require bins to be based on adjacent markers only
cutoff	Max RF allowed before starting a new bin
consensusProbability	Proportion of genotypes within FDP groups which must match for imputation to occur.
missingCutoff	Proportion of missing data allowed within markers before not using to create haplotypes

Value

A binned object of class binmpcross

Note

Markers are assigned to a bin if there is zero recombination between any of the markers within the bin (or correlation of 1). Next, a three-step process is performed to create the new set of bin markers. First, markers within a bin are grouped based on founder distribution pattern (FDP). Second, for each FDP, a single representative marker is chosen, with missing values imputed from all markers sharing that FDP. Third, haplotypes formed from these representative markers are used to replace genotypes for the bin marker.

See Also

link{mpexpand}

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.