phaseReport: Best/all hapltype groups for a genotype

In mlPhaser: Multi-Locus Haplotype Phasing

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).

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.

Value

A data.frame of results...

See Also

getValidHaploGroups

Examples

# 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")

mlPhaser documentation built on May 2, 2019, 7:59 a.m.