Package index • sequoia

Input

Read, convert and check input data

GenoConvert(): Convert Genotype Data

LHConvert(): Extract Sex and Birth Year from PLINK File

CheckGeno(): Check Genotype Matrix

SnpStats(): SNP Summary Statistics

CalcMaxMismatch(): Maximum Number of Mismatches

Simulate

Simulate genotype data assuming independent SNPs

SimGeno(): Simulate Genotypes

MkGenoErrors(): Simulate Genotyping Errors

Inherit_patterns: Inheritance patterns

AgePrior

See ageprior vignette for details

MakeAgePrior(): Age Priors

PlotAgePrior(): Plot Age Priors

CalcBYprobs(): Birth year probabilities

Pedigree reconstruction

The core of the package, see main vignette for details

sequoia(): Pedigree Reconstruction

GetMaybeRel(): Find Putative Relatives

Likelihood (ratios)

CalcOHLLR(): Calculate OH and LLR for a pedigree

CalcPairLL(): Calculate Likelihoods for Alternative Relationships

PlotPairLL(): Plot Pair Log10-Likelihoods

GetLLRAge(): LLR-age from Ageprior Matrix

LLtoProb(): transform log-likelihoods to probabilities

CalcParentProbs(): Calculate assignment probabilities

Pedigree check

These functions can be applied to any pedigree, no genetic data needed

EstConf(): Confidence Probabilities

GetRelM(): Matrix with Pairwise Relationships

PlotRelPairs(): Plot Pairwise Relationships

SummarySeq(): Summarise Sequoia Output or Pedigree

PlotSeqSum(): Plot Summary Overview of sequoia Output

getAssignCat(): Assignability of Reference Pedigree

getGenerations(): Count Generations

GetAncestors(): Get ancestors

GetDescendants(): Get descendants

CalcRped(): Calculate Pedigree Relatedness

Compare 2 pedigrees

PedCompare(): Compare Two Pedigrees

PlotPedComp(): Visualise PedCompare Output

ComparePairs(): Compare Pairwise Relationships

Miscellaneous

PedPolish(): Fix Pedigree

ErrToM(): Generate Genotyping Error Matrix

Err_RADseq(): Convert Genotyping Error Rates from per-allele to per-locus

writeSeq(): Write Sequoia Output to File

writeColumns(): Write Data to a File Column-wise

FindFamilies(): Assign Family IDs

PedStripFID(): Back-transform IDs

Example data

Ped_HSg5: Example pedigree: 'HSg5'

LH_HSg5: Example life history file: 'HSg5'

SimGeno_example: Example genotype file: 'HSg5'

Geno_HSg5: Example genotype file: 'HSg5'

SeqOUT_HSg5: Example output from pedigree inference: 'HSg5'

Ped_griffin: Example pedigree: griffins

LH_griffin: Example life history data: griffins

FieldMums_griffin: Example field-observed mothers: griffins

Geno_griffin: Example genotype file: Griffins

SeqOUT_griffin: Example output from pedigree inference: griffins

Conf_griffin: Example output from estimating confidence probabilities: griffins

MaybeRel_griffin: Example output from check for relatives: griffins

Deprecated

DyadCompare(): Compare Dyads (DEPRECATED)

EstEr(): Estimate genotyping error rate (REMOVED; will be re-implemented)