# Pedigree Inference from SNPs

## Documentation for package ‘sequoia’ version 3.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

CalcBYprobs | Birth year probabilities
CalcMaxMismatch | Maximum Number of Mismatches
CalcOHLLR | Calculate OH and LLR for a pedigree
CalcPairLL | Calculate Likelihoods for Alternative Relationships
CalcParentProbs | Calculate assignment probabilities
CalcRped | Calculate Pedigree Relatedness
CheckGeno | Check Genotype Matrix
ComparePairs | Compare Pairwise Relationships
Conf_griffin | Example output from estimating confidence probabilities: griffins
CountOH | Count opposing homozygous SNPs between pairs of individuals
DyadCompare | Compare Dyads (DEPRECATED)
ErrToM | Generate Genotyping Error Matrix
Err_RADseq | Convert Genotyping Error Rates from per-allele to per-locus
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'
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'
LLtoProb | transform log-likelihoods to probabilities
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
PlotPropAssigned | Plot proportion of individuals that has a parent assigned
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