mergeAlleleAssignments: Merge Allele Assignment Matrices

In polysat: Tools for Polyploid Microsatellite Analysis

Merge Allele Assignment Matrices

Description

In cases where multiple populations are used separately to assign alleles to homeologous loci, mergeAlleleAssignments is used to consolidate the results.

Usage

mergeAlleleAssignments(x)

Arguments

x	A list, where each element is in the format of results produced by catalanAlleles or testAlGroups; see example.

Value

A list in similar format to x, but with only one element per locus.

Author(s)

Lindsay V. Clark

See Also

testAlGroups, catalanAlleles, recodeAllopoly

Examples

# List of allele assignment results for this example; normally these
# would be produced by other functions evaluating a genetic dataset.
# The example below is for an allotetraploid.

# Locus L1 is a well-behaved locus with no homoplasy.
myresults <- list(list(locus="L1", SGploidy=2,
                  assignments=matrix(c(1,0,0,1,1,0,0,1,0,1), nrow=2,
                  ncol=5, dimnames=list(NULL,
                  c("124","128","130","134","138")))),
                  list(locus="L1", SGploidy=2,
                  assignments=matrix(c(0,1,1,0,1,0,0,1), nrow=2, ncol=4,
                  dimnames=list(NULL, c("124","128","132","140")))),
                  list(locus="L1", SGploidy=2,
                  assignments=matrix(c(0,1,1,0,0,1,1,0), nrow=2, ncol=4,
                  dimnames=list(NULL, c("126","128","130","132")))),
# Locus L2 is unresolvable because there are no shared alleles between
# populations.
                  list(locus="L2", SGploidy=2,
                  assignments=matrix(c(1,0,1,0,0,1), nrow=2, ncol=3,
                  dimnames=list(NULL, c("205","210","225")))),
                  list(locus="L2", SGploidy=2,
                  assignments=matrix(c(1,0,0,1,0,1,1,0), nrow=2, ncol=4,
                  dimnames=list(NULL, c("195","215","220","230")))),
# Locus L3 has homoplasy that makes it unresolvable.
                  list(locus="L3", SGploidy=2,
                  assignments=matrix(c(1,0,0,1,0,1,1,0), nrow=2, ncol=4,
                  dimnames=list(NULL, c("153","159","168","171")))),
                  list(locus="L3", SGploidy=2,
                  assignments=matrix(c(1,0,0,1,1,0,0,1), nrow=2, ncol=4,
                  dimnames=list(NULL, c("153","156","165","171")))),
# Locus L4 has homoplasy, but the results can still be merged.
                  list(locus="L4", SGploidy=2,
                  assignments=matrix(c(1,0,1,0,0,1,0,1,0,1), nrow=2, ncol=5,
                  dimnames=list(NULL, c("242","246","254","260","264")))),
                  list(locus="L4", SGploidy=2,
                  assignments=matrix(c(1,0,0,1,1,0,0,1,0,1), nrow=2, ncol=5,
                  dimnames=list(NULL, c("242","246","250","254","260"))))
                  )
myresults

# merge within loci
mergedresults <- mergeAlleleAssignments(myresults)
mergedresults

polysat documentation built on Aug. 23, 2022, 5:07 p.m.