genClones: Find and report genotype clones

In ASMap: Linkage Map Construction using the MSTmap Algorithm

Find and report genotype clones

Description

Find and report genotype clones for qtl objects.

Usage

genClones(object, chr, tol = 0.9, id = "Genotype")

Arguments

object	An qtl object object with any class structure.
chr	A character string of linkage group names.
tol	Pairs of genotypes with a proporion of matching alleles above this tolerance will be returned.
id	Character string defining the column of object$pheno containing the genotype names.

Details

This function extends the functionality of comparegeno in the qtl package by providing breakdown statistics for the pairs of genotypes that have a proportion of matching alleles above tol.

Value

A list is returned with the matrix from comparegeno as an element cgm and the breakdown statistics for returned genotype pairs in cgd. Specifically, the statistics contain a "group" column which determines the clonal group the pair of genotypes belongs to.

Author(s)

Julian Taylor

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

See Also

comparegeno and fixClones

Examples

data(mapDH, package = "ASMap")

gc <- genClones(mapDH)

ASMap documentation built on Nov. 1, 2024, 9:08 a.m.