Description Usage Arguments Details Value
View source: R/phasing_codes_3_25_2014.R
compute compound gentoype for trios from sequencing data
1 2 3 4 | FamilyPhase(parent.genotype, child.genotype)
FamilyPhaseII(parent.genotype, child.genotype)
FamilyPhaseIII(parent.genotype, child.genotype)
PairPhase(paternal.genotype, child.genotype)
|
parent.genotype |
matrix, parents genotype |
child.genotype |
vector, child gentoype |
paternal.genotype |
vector, genotype of one parent |
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
3 elements vector: paternal compound genotype, maternal compound genotype and child's compound genotype
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