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sequoia (version 3.0.3)

Pedigree Inference from SNPs

Description

Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) () for more information.

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Version

Install

install.packages('sequoia')

Monthly Downloads

732

Version

3.0.3

License

GPL-2

Maintainer

Jisca Huisman

Last Published

August 19th, 2025

Functions in sequoia (3.0.3)

DoErrors

Fortran Simulate Genotyping Errors
Err_RADseq

Convert Genotyping Error Rates from per-allele to per-locus
DyadCompare

Compare Dyads (DEPRECATED)
ComparePairs

Compare Pairwise Relationships
DuplicateCheck

Check Data for Duplicates.
EstEr

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

Check if input parameters are valid
ErrToM

Generate Genotyping Error Matrix
EstConf

Confidence Probabilities
Conf_griffin

Example output from estimating confidence probabilities: griffins
FoldSibGPs

Fold IDs of Sibship Grandparents
GetLLRAge

LLR-age from Ageprior Matrix
FindFamilies

Assign Family IDs
GetAncestors

Get ancestors
GetDescendants

Get descendants
GenoConvert

Convert Genotype Data
FortifyPairs

Make Pairs Fortran Compatible
FieldMums_griffin

Example field-observed mothers: griffins
Geno_HSg5

Example genotype file: 'HSg5'
Geno_griffin

Example genotype file: Griffins
Inherit_patterns

Inheritance patterns
LLtoProb

transform log-likelihoods to probabilities
LH_griffin

Example life history data: griffins
LHConvert

Extract Sex and Birth Year from PLINK File
MakeAgePrior

Age Priors
GetRelM

Matrix with Pairwise Relationships
GetMaybeRel

Find Putative Relatives
GetRelA

Array with Pairwise Relationships
LLRplot

Scatter Plot of Pair LLRs
LH_HSg5

Example life history file: 'HSg5'
ParamToSpecs

PARAM to Specs
PedCompare

Compare Two Pedigrees
MkGenoErrors

Simulate Genotyping Errors
PedPolish

Fix Pedigree
MkFortParams

PARAM to FortPARAM
OHperSNP

Estimate Genotyping Error Rate
MergeFill

Special Merge
MkAPdefault

Make default 1/0 ageprior
NumToID

Change Numeric Pedigree back to Character Pedigree
MaybeRel_griffin

Example output from check for relatives: griffins
PlotAgePrior

Plot Age Priors
PlotSeqSum

Plot Summary Overview of sequoia Output
PedToNum

Turn Character Pedigree into Numeric Pedigree
PlotRelPairs

Plot Pairwise Relationships
PedStripFID

Back-transform IDs
PlotPedComp

Visualise PedCompare Output
PlotPairLL

Plot Pair Log10-Likelihoods
PlotSnpStats

plot SnpStats results
Ped_HSg5

Example pedigree: 'HSg5'
Ped_griffin

Example pedigree: griffins
SimGeno

Simulate Genotypes
SnpStats

SNP Summary Statistics
SelectNotSampled

select non-genotyped parents
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
SibMatch

Find the closest matching inferred sibship to a true sibship
ReOrderDums

Re-order likelihood vector
SimGeno_example

Example genotype file: 'HSg5'
sequoia

Pedigree Reconstruction
SeqOUT_griffin

Example output from pedigree inference: griffins
SpecsToParam

Specs to PARAM
VennSquares

Square Venn diagram
SmoothAP

Smooth out dips in ageprior matrix
mtSame2Dif

Check and recode mtSame matrix
SummarySeq

Summarise Sequoia Output or Pedigree
getAssignCat

Assignability of Reference Pedigree
getGenerations

Count Generations
writeColumns

Write Data to a File Column-wise
writeSeq

Write Sequoia Output to File
SeqOUT_HSg5

Example output from pedigree inference: 'HSg5'
tryCatch.W.E

tryCatch both warnings (with value) and errors
rc

Find siblings
Vcomp

Compare two vectors
orderLH

Order Lifehistory Data
CheckLH

Check LifeHistData
CalcRped

Calculate Pedigree Relatedness
CalcBYprobs

Birth year probabilities
CheckGeno

Check Genotype Matrix
CalcParentProbs

Calculate assignment probabilities
CalcMaxMismatch

Maximum Number of Mismatches
CalcOHLLR

Calculate OH and LLR for a pedigree
CalcPairLL

Calculate Likelihoods for Alternative Relationships
CalcCorners

Corner coordinates
CheckAP

check AgePrior