Pedigree Inference from SNPs


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Documentation for package ‘sequoia’ version 2.3.3

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CalcBYprobs Birth year probabilities
CalcMaxMismatch Maximum Number of Mismatches
CalcOHLLR Calculate OH and LLR
CalcPairLL Calculate Likelihoods for Alternative Relationships
CalcRped Calculate Pedigree Relatedness
CheckGeno Check Genotype Matrix
ComparePairs Compare Pairwise Relationships
DyadCompare Compare Dyads
ErrToM Generate Genotyping Error Matrix
EstConf Confidence Probabilities
FieldMums_griffin Example field-observed mothers: griffins
FindFamilies Assign Family IDs
GenoConvert Convert Genotype Data
getAssignCat Assignability of Reference Pedigree
getGenerations Count Generations
GetLLRAge LLR-age from Ageprior Matrix
GetMaybeRel Find Putative Relatives
GetRelM Matrix with Pairwise Relationships
Inherit Inheritance patterns
LHConvert Extract Sex and Birth Year from PLINK File
LH_griffin Example lifehistory data: griffins
LH_HSg5 Example life history file
MakeAgePrior Age Priors
MkGenoErrors Simulate Genotyping Errors
PedCompare Compare Two Pedigrees
PedPolish Fix Pedigree
PedStripFID Back-transform IDs
Ped_griffin Example pedigree: griffins
Ped_HSg5 Example pedigree
PlotAgePrior Plot Age Priors
PlotPairLL Plot Pair Log10-Likelihoods
PlotPedComp Visualise PedCompare Output
PlotRelPairs Plot Pairwise Relationships
SeqOUT_griffin Example sequoia output (griffins)
sequoia Pedigree Reconstruction
SimGeno Simulate Genotypes
SimGeno_example Example genotype file
SnpStats SNP Summary Statistics
SummarySeq Summarise Sequoia Output or Pedigree
tryCatch.W.E tryCatch both warnings (with value) and errors
writeColumns Write Data to a File Column-wise
writeSeq Write Sequoia Output to File