Pedigree Inference from SNPs

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Documentation for package ‘sequoia’ version 2.4.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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
Conf_griffin	Example output from estimating confidence probabilities: griffins
DyadCompare	Compare Dyads (DEPRECATED)
ErrToM	Generate Genotyping Error Matrix
EstConf	Confidence Probabilities
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'
getAssignCat	Assignability of Reference Pedigree
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
sequoia_report	Sequoia report
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