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sequoia (version 3.1.3)

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

654

Version

3.1.3

License

GPL-2

Maintainer

Jisca Huisman

Last Published

November 18th, 2025

Functions in sequoia (3.1.3)

CalcMaxMismatch

Maximum Number of Mismatches
CalcBYprobs

Birth year probabilities
CheckGeno

Check Genotype Matrix
CalcCorners

Corner coordinates
CalcPairLL

Calculate Likelihoods for Alternative Relationships
CalcRped

Calculate Pedigree Relatedness
CalcParentProbs

Calculate assignment probabilities
CalcOHLLR

Calculate OH and LLR for a pedigree
CheckLH

Check LifeHistData
CheckAP

check AgePrior
DoErrors

Fortran Simulate Genotyping Errors
ComparePairs

Compare Pairwise Relationships
CountOH

Count opposing homozygous SNPs between pairs of individuals
CheckParams

Check if input parameters are valid
DuplicateCheck

Check Data for Duplicates.
ErrToM

Generate Genotyping Error Matrix
DyadCompare

Compare Dyads (DEPRECATED)
Err_RADseq

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

Example output from estimating confidence probabilities: griffins
EstConf

Confidence Probabilities
EstEr

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

Assign Family IDs
GenoConvert

Convert Genotype Data
GetAncestors

Get ancestors
GetDescendants

Get descendants
FortifyPairs

Make Pairs Fortran Compatible
FoldSibGPs

Fold IDs of Sibship Grandparents
Geno_griffin

Example genotype file: Griffins
FieldMums_griffin

Example field-observed mothers: griffins
Geno_HSg5

Example genotype file: 'HSg5'
Inherit_patterns

Inheritance patterns
LHConvert

Extract Sex and Birth Year from PLINK File
GetLLRAge

LLR-age from Ageprior Matrix
LH_griffin

Example life history data: griffins
GetRelA

Array with Pairwise Relationships
LLRplot

Scatter Plot of Pair LLRs
LH_HSg5

Example life history file: 'HSg5'
GetMaybeRel

Find Putative Relatives
LLtoProb

transform log-likelihoods to probabilities
MaybeRel_griffin

Example output from check for relatives: griffins
MakeAgePrior

Age Priors
MkGenoErrors

Simulate Genotyping Errors
PedCompare

Compare Two Pedigrees
ParamToSpecs

PARAM to Specs
MkFortParams

PARAM to FortPARAM
NumToID

Change Numeric Pedigree back to Character Pedigree
GetRelM

Matrix with Pairwise Relationships
PedPolish

Fix Pedigree
PedStripFID

Back-transform IDs
OHperSNP

Estimate Genotyping Error Rate
PlotPedComp

Visualise PedCompare Output
PlotPairLL

Plot Pair Log10-Likelihoods
Ped_griffin

Example pedigree: griffins
PlotAgePrior

Plot Age Priors
PlotRelPairs

Plot Pairwise Relationships
PlotPropAssigned

Plot proportion of individuals that has a parent assigned
PedToNum

Turn Character Pedigree into Numeric Pedigree
SimGeno

Simulate Genotypes
MkAPdefault

Make default 1/0 ageprior
MergeFill

Special Merge
Ped_HSg5

Example pedigree: 'HSg5'
Vcomp

Compare two vectors
SeqOUT_griffin

Example output from pedigree inference: griffins
SnpStats

SNP Summary Statistics
SeqOUT_HSg5

Example output from pedigree inference: 'HSg5'
SimGeno_example

Example genotype file: 'HSg5'
VennSquares

Square Venn diagram
SmoothAP

Smooth out dips in ageprior matrix
SelectNotSampled

select non-genotyped parents
ReOrderDums

Re-order likelihood vector
writeColumns

Write Data to a File Column-wise
SummarySeq

Summarise Sequoia Output or Pedigree
SpecsToParam

Specs to PARAM
SibMatch

Find the closest matching inferred sibship to a true sibship
orderLH

Order Lifehistory Data
mtSame2Dif

Check and recode mtSame matrix
tryCatch.W.E

tryCatch both warnings (with value) and errors
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
getGenerations

Count Generations
getAssignCat

Assignability of Reference Pedigree
PlotSeqSum

Plot Summary Overview of sequoia Output
sequoia

Pedigree Reconstruction
writeSeq

Write Sequoia Output to File
PlotSnpStats

plot SnpStats results
rc

Find siblings