phaseReport: Best/all hapltype groups for a genotype

Description

Attempts to find best/all haplotype groups that fully explain observed multi-locus genotypes.

Usage

phaseReport(genotypes, haplotypes, haploFreqs, outFormat = "all")

Arguments

genotypes

The table/list of genotypes

haplotypes

The table/list of candidate haplotypes

haploFreqs

The frequencies of haplotypes as a named vector.

outFormat

Whether to output all valid haplotype groups or just the best (based on joint probability).

Value

A data.frame of results...

Details

This wrapper function takes a set of genotypes, a set of haplotypes and a set of haplotype frequencies and attempts to report either all groups or just the single most likely group of known haplotypes that fully explains each observed genotype.

Examples

Run this code

# create a data frame to store alleles of haplotypes. Columns are loci.
haplotypes <- data.frame(	A= c("a","b","c","a","b","c","b"),
					B= c("a","b","c","b","c","a","a"),
					C= c("a","b","c","b","c","a","a") )
# give the haplotypes sensible names as rownames.
rownames(haplotypes) <- apply(haplotypes, 1, paste,sep="" , collapse="")
# Create a named vector of haplotype frequencies.
haploFreqs <- c(0.4, 0.3, 0.15, 0.07,0.05, 0.02, 0.01)
names(haploFreqs) <- rownames(haplotypes)
# load a genotype as a table
thisGenotype <- data.frame(A.1="a", A.2="b", B.1="a", B.2="b",C.1="a", C.2="b")
phaseReport(thisGenotype,haplotypes)
# use haplotype frequencies to rank candidate haplotype groups.
phaseReport(thisGenotype,haplotypes, haploFreqs)
# return only the best haplotype group for each genotype.
phaseReport(thisGenotype,haplotypes, haploFreqs, outFormat="top")

# simulate a set of genootypes
my.genotypes <- simGenoFromHaplo(haploTable=haplotypes, haploFreqs=haploFreqs , n=20, ploidy=2)
# get phase report on all genotypes
phaseReport(my.genotypes,haplotypes, haploFreqs, outFormat="all")	# outFormat="all" is the default
phaseReport(my.genotypes,haplotypes, haploFreqs, outFormat="top")