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sequoia (version 2.5.6)

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

757

Version

2.5.6

License

GPL-2

Maintainer

Jisca Huisman

Last Published

April 22nd, 2023

Functions in sequoia (2.5.6)

DyadCompare

Compare Dyads (DEPRECATED)
EstErr

Estimate Genotyping Error Rate
EstConf

Confidence Probabilities
CheckParams

Check if input parameters are valid
ComparePairs

Compare Pairwise Relationships
Conf_griffin

Example output from estimating confidence probabilities: griffins
GenoConvert

Convert Genotype Data
CountAgeDif

Tabulate Age Differences
DuplicateCheck

Check Data for Duplicates.
DoErrors

Fortran Simulate Genotyping Errors
ErrToM

Generate Genotyping Error Matrix
Geno_griffin

Example genotype file: Griffins
Geno_HSg5

Example genotype file: 'HSg5'
GetDescendants

Get descendants
FindFamilies

Assign Family IDs
FoldSibGPs

Fold IDs of Sibship Grandparents
GetAncestors

Get ancestors
FieldMums_griffin

Example field-observed mothers: griffins
FortifyPairs

Make Pairs Fortran Compatible
GetDummifiable

Dummifiable IDs
GetRelM

Matrix with Pairwise Relationships
LH_griffin

Example life history data: griffins
GetRelA

Array with Pairwise Relationships
GetLLRAge

LLR-age from Ageprior Matrix
LH_HSg5

Example life history file: 'HSg5'
Inherit_patterns

Inheritance patterns
LHConvert

Extract Sex and Birth Year from PLINK File
MakeAgePrior

Age Priors
LLRplot

Scatter Plot of Pair LLRs
GetMaybeRel

Find Putative Relatives
MaybeRel_griffin

Example output from check for relatives: griffins
PedCompare

Compare Two Pedigrees
PedStripFID

Back-transform IDs
PedToNum

Turn Character Pedigree into Numeric Pedigree
ParamToSpecs

PARAM to Specs
NumToID

Change Numeric Pedigree back to Character Pedigree
PedPolish

Fix Pedigree
MkFortParams

PARAM to FortPARAM
MergeFill

Special Merge
MkGenoErrors

Simulate Genotyping Errors
PlotSeqSum

Plot Summary Overview of sequoia Output
SeqOUT_griffin

Example output from pedigree inference: griffins
PlotSnpStats

plot SnpStats results
PlotPedComp

Visualise PedCompare Output
Ped_griffin

Example pedigree: griffins
Ped_HSg5

Example pedigree: 'HSg5'
SeqOUT_HSg5

Example output from pedigree inference: 'HSg5'
PlotAgePrior

Plot Age Priors
PlotRelPairs

Plot Pairwise Relationships
VennSquares

Square Venn diagram
SummarySeq

Summarise Sequoia Output or Pedigree
Vcomp

Compare two vectors
PlotPairLL

Plot Pair Log10-Likelihoods
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
SimGeno

Simulate Genotypes
SibMatch

Find the closest matching inferred sibship to a true sibship
SimGeno_example

Example genotype file: 'HSg5'
writeSeq

Write Sequoia Output to File
SpecsToParam

Specs to PARAM
SnpStats

SNP Summary Statistics
getGenerations

Count Generations
getAssignCat

Assignability of Reference Pedigree
writeColumns

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

tryCatch both warnings (with value) and errors
orderLH

Order Lifehistory Data
rc

Find siblings
sequoia

Pedigree Reconstruction
CheckGeno

Check Genotype Matrix
CalcOHLLR

Calculate OH and LLR for a pedigree
CalcRped

Calculate Pedigree Relatedness
CheckAP

check AgePrior
CalcBYprobs

Birth year probabilities
CheckLH

Check LifeHistData
CalcCorners

Corner coordinates
CalcMaxMismatch

Maximum Number of Mismatches
CalcPairLL

Calculate Likelihoods for Alternative Relationships
CalcChi2

Chi-square Test on Observed vs Expected Genotypes