Pedigree Inference from SNPs


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Documentation for package ‘sequoia’ version 2.11.2

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CalcBYprobs Birth year probabilities
CalcMaxMismatch Maximum Number of Mismatches
CalcOHLLR Calculate OH and LLR for a pedigree
CalcPairLL Calculate Likelihoods for Alternative Relationships
CalcRped Calculate Pedigree Relatedness
CheckGeno Check Genotype Matrix
ComparePairs Compare Pairwise Relationships
Conf_griffin Example output from estimating confidence probabilities: griffins
DyadCompare Compare Dyads (DEPRECATED)
ErrToM Generate Genotyping Error Matrix
EstConf Confidence Probabilities
EstEr Estimate genotyping error rate (REMOVED; will be re-implemented)
FieldMums_griffin Example field-observed mothers: griffins
FindFamilies Assign Family IDs
GenoConvert Convert Genotype Data
Geno_griffin Example genotype file: Griffins
Geno_HSg5 Example genotype file: 'HSg5'
GetAncestors Get ancestors
getAssignCat Assignability of Reference Pedigree
GetDescendants Get descendants
getGenerations Count Generations
GetLLRAge LLR-age from Ageprior Matrix
GetMaybeRel Find Putative Relatives
GetRelM Matrix with Pairwise Relationships
Inherit_patterns Inheritance patterns
LHConvert Extract Sex and Birth Year from PLINK File
LH_griffin Example life history data: griffins
LH_HSg5 Example life history file: 'HSg5'
MakeAgePrior Age Priors
MaybeRel_griffin Example output from check for relatives: griffins
MkGenoErrors Simulate Genotyping Errors
PedCompare Compare Two Pedigrees
PedPolish Fix Pedigree
PedStripFID Back-transform IDs
Ped_griffin Example pedigree: griffins
Ped_HSg5 Example pedigree: 'HSg5'
PlotAgePrior Plot Age Priors
PlotPairLL Plot Pair Log10-Likelihoods
PlotPedComp Visualise PedCompare Output
PlotRelPairs Plot Pairwise Relationships
PlotSeqSum Plot Summary Overview of sequoia Output
SeqOUT_griffin Example output from pedigree inference: griffins
SeqOUT_HSg5 Example output from pedigree inference: 'HSg5'
sequoia Pedigree Reconstruction
SimGeno Simulate Genotypes
SimGeno_example Example genotype file: 'HSg5'
SnpStats SNP Summary Statistics
SummarySeq Summarise Sequoia Output or Pedigree
writeColumns Write Data to a File Column-wise
writeSeq Write Sequoia Output to File