coreTDT (version 1.0)

FamilyPhase: Phasing trios

Description

compute compound gentoype for trios from sequencing data

Usage

FamilyPhase(parent.genotype, child.genotype)
FamilyPhaseII(parent.genotype, child.genotype)
FamilyPhaseIII(parent.genotype, child.genotype)
PairPhase(paternal.genotype, child.genotype)

Arguments

parent.genotype

matrix, parents genotype

child.genotype

vector, child gentoype

paternal.genotype

vector, genotype of one parent

Value

3 elements vector: paternal compound genotype, maternal compound genotype and child's compound genotype

Details

PairPhase: sharing analysis between one parent and child FamilyPhase: compute cpmpound genotype for trios when parents do not share any variants FamilyPhaseII: compute cpmpound genotype for trios. when parents share heterozygous variants, remove shared variants and perform test FamilyPhaseIII: compute cpmpound genotype for trios. when parents share heterozygous variants, set family as missing data,used in current analysis