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sequoia (version 2.4.1)

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

1,235

Version

2.4.1

License

GPL-2

Maintainer

Jisca Huisman

Last Published

January 8th, 2023

Functions in sequoia (2.4.1)

CalcCorners

Corner coordinates
CalcRped

Calculate Pedigree Relatedness
CalcBYprobs

Birth year probabilities
CalcChi2

Chi-square Test on Observed vs Expected Genotypes
CalcOHLLR

Calculate OH and LLR
CalcMaxMismatch

Maximum Number of Mismatches
CheckGeno

Check Genotype Matrix
CalcPairLL

Calculate Likelihoods for Alternative Relationships
CheckAP

check AgePrior
CheckLH

Check LifeHistData
CheckParams

Check if input parameters are valid
DyadCompare

Compare Dyads (DEPRECATED)
ErrToM

Generate Genotyping Error Matrix
DoErrors

Fortran Simulate Genotyping Errors
DuplicateCheck

Check Data for Duplicates.
EstConf

Confidence Probabilities
ComparePairs

Compare Pairwise Relationships
CountAgeDif

Tabulate Age Differences
EstErr

Estimate Genotyping Error Rate
Conf_griffin

Example output from estimating confidence probabilities: griffins
FindFamilies

Assign Family IDs
FieldMums_griffin

Example field-observed mothers: griffins
GenoConvert

Convert Genotype Data
Geno_HSg5

Example genotype file: 'HSg5'
FoldSibGPs

Fold IDs of Sibship Grandparents
GetLLRAge

LLR-age from Ageprior Matrix
GetMaybeRel

Find Putative Relatives
FortifyPairs

Make Pairs Fortran Compatible
LH_griffin

Example life history data: griffins
LH_HSg5

Example life history file: 'HSg5'
GetRelM

Matrix with Pairwise Relationships
GetRelA

Array with Pairwise Relationships
MergeFill

Special Merge
LHConvert

Extract Sex and Birth Year from PLINK File
MaybeRel_griffin

Example output from check for relatives: griffins
GetDummifiable

Dummifiable IDs
Inherit_patterns

Inheritance patterns
Geno_griffin

Example genotype file: Griffins
MakeAgePrior

Age Priors
LLRplot

Scatter Plot of Pair LLRs
PedCompare

Compare Two Pedigrees
PedPolish

Fix Pedigree
Ped_griffin

Example pedigree: griffins
Ped_HSg5

Example pedigree: 'HSg5'
PedStripFID

Back-transform IDs
PedToNum

Turn Character Pedigree into Numeric Pedigree
SeqOUT_HSg5

Example output from pedigree inference: 'HSg5'
SeqOUT_griffin

Example output from pedigree inference: griffins
NumToID

Change Numeric Pedigree back to Character Pedigree
ParamToSpecs

PARAM to Specs
PlotSeqSum

Plot Summary Overview of sequoia Output
MkGenoErrors

Simulate Genotyping Errors
PlotPedComp

Visualise PedCompare Output
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
PlotSnpStats

plot SnpStats results
MkFortParams

PARAM to FortPARAM
PlotRelPairs

Plot Pairwise Relationships
PlotAgePrior

Plot Age Priors
PlotPairLL

Plot Pair Log10-Likelihoods
SibMatch

Find the closest matching inferred sibship to a true sibship
getGenerations

Count Generations
SnpStats

SNP Summary Statistics
SimGeno

Simulate Genotypes
SummarySeq

Summarise Sequoia Output or Pedigree
getAssignCat

Assignability of Reference Pedigree
VennSquares

Square Venn diagram
orderLH

Order Lifehistory Data
SimGeno_example

Example genotype file: 'HSg5'
Vcomp

Compare two vectors
sequoia

Pedigree Reconstruction
rc

Find siblings
SpecsToParam

Specs to PARAM
sequoia_report

Sequoia report
writeSeq

Write Sequoia Output to File
writeColumns

Write Data to a File Column-wise
tryCatch.W.E

tryCatch both warnings (with value) and errors