Pedigree Inference from SNPs


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Documentation for package ‘sequoia’ version 2.0.7

Help Pages

CalcMaxMismatch Maximum number of mismatches
CalcOHLLR calculate OH and LLR
CheckGeno check GenoM
ComparePairs Comparison of all pairwise relationships in 2 pedigrees
DyadCompare Compare dyads
ErrToM Generate error matrix
EstConf Estimate confidence probability
FindFamilies Assign family IDs
GenoConvert Convert genotype data
getAssignCat Assignability of reference pedigree
GetMaybeRel Find putative relatives
GetRelCat Pairwise relationship
Inherit Inheritance patterns
LHConvert Extract sex and birthyear from PLINK file
LH_HSg5 Example life history file
MakeAgePrior Age priors
MkGenoErrors Simulate genotyping errors
PedCompare Compare two Pedigrees
PedPolish Pedigree fix
PedStripFID backtransform IDs
Ped_griffin Example pedigree: griffins
Ped_HSg5 Example pedigree
PlotAgePrior Plot age priors
SeqOUT_griffin Example sequoia output (griffins)
sequoia Pedigree Reconstruction
SimGeno Simulated genotypes
SimGeno_example Example genotype file
SnpStats SNP summary statistics
SummarySeq Summarise sequoia output or pedigree
writeColumns write data to a file column-wise
writeSeq write sequoia output to excel or text files