mlPhaser (version 0.01)

getValidHaploGroups: Get haplo groups for a genotype

Description

Get all valid groups of haplotypes that fully explain a genotype.

Usage

getValidHaploGroups(genotype, haplotypes)

Arguments

genotype

The genotype in question. Can be data.frame or list of lists format

haplotypes

The set of candidate haplotypes.

Value

A list of valid haplotype groups (each itself a list of haplotypes).

Details

Wrapper function to set up and control the recursive search for groups of haplotyps, each of which are consistent with the genotype in question. Makes use of recursion via the function recurseHaplos

See Also

phaseReport

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="")
# 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")
# find groups of haplotypes as a list of lists
my.valid.groups <- getValidHaploGroups(thisGenotype,haplotypes)
# look at the list structure of the valid groups list
str(my.valid.groups)
# see phaseReport() for more friendly function