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sequoia

Pedigree Inference from SNPs

Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.

Functions (70)

CalcBYprobs

Birth year probabilities

CalcChi2

Chi-square Test on Observed vs Expected Genotypes

CalcCorners

Corner coordinates

CalcMaxMismatch

Maximum Number of Mismatches

CalcOHLLR

Calculate OH and LLR

CalcPairLL

Calculate Likelihoods for Alternative Relationships

CalcRped

Calculate Pedigree Relatedness

CheckAP

check AgePrior

CheckGeno

Check Genotype Matrix

CheckLH

Check LifeHistData

CheckParams

Check if input parameters are valid

ComparePairs

Compare Pairwise Relationships

CountAgeDif

Tabulate Age Differences

DoErrors

Fortran Simulate Genotyping Errors

DuplicateCheck

Check Data for Duplicates.

DyadCompare

Compare Dyads

ErrToM

Generate Genotyping Error Matrix

EstConf

Confidence Probabilities

EstErr

Estimate Genotyping Error Rate

FieldMums_griffin

Example field-observed mothers: griffins

FindFamilies

Assign Family IDs

FoldSibGPs

Fold IDs of Sibship Grandparents

FortifyPairs

Make Pairs Fortran Compatible

GenoConvert

Convert Genotype Data

GetDummifiable

Dummifiable IDs

GetLLRAge

LLR-age from Ageprior Matrix

GetMaybeRel

Find Putative Relatives

GetRelA

Array with Pairwise Relationships

GetRelM

Matrix with Pairwise Relationships

Inherit

Inheritance patterns

LHConvert

Extract Sex and Birth Year from PLINK File

LH_HSg5

Example life history file

LH_griffin

Example lifehistory data: griffins

LLRplot

Scatter Plot of Pair LLRs

MakeAgePrior

Age Priors

MergeFill

Special Merge

MkFortParams

PARAM to FortPARAM

MkGenoErrors

Simulate Genotyping Errors

NumToID

Change Numeric Pedigree back to Character Pedigree

ParamToSpecs

PARAM to Specs

PedCompare

Compare Two Pedigrees

PedPolish

Fix Pedigree

PedStripFID

Back-transform IDs

PedToNum

Turn Character Pedigree into Numeric Pedigree

Ped_HSg5

Example pedigree

Ped_griffin

Example pedigree: griffins

PlotAgePrior

Plot Age Priors

PlotPairLL

Plot Pair Log10-Likelihoods

PlotPedComp

Visualise PedCompare Output

PlotRelPairs

Plot Pairwise Relationships

SeqOUT_griffin

Example sequoia output (griffins)

SeqParSib

Fortran Wrapper for Pedigree Reconstruction

SibMatch

Find the closest matching inferred sibship to a true sibship

SimGeno

Simulate Genotypes

SimGeno_example

Example genotype file

SnpStats

SNP Summary Statistics

SpecsToParam

Specs to PARAM

SummarySeq

Summarise Sequoia Output or Pedigree

Vcomp

Compare two vectors

VennSquares

Square Venn diagram

getAssignCat

Assignability of Reference Pedigree

getGDO

get individual category: genotyped, dummy, observed

getGenerations

Count Generations

orderLH

Order Lifehistory Data

plot.seq

Plot Summary Overview of sequoia Output

Find siblings

sequoia

Pedigree Reconstruction

tryCatch.W.E

tryCatch both warnings (with value) and errors

writeColumns

Write Data to a File Column-wise

writeSeq

Write Sequoia Output to File

sequoia

Pedigree Inference from SNPs

v2.3.3

GPL-2

Authors

Jisca Huisman [aut, cre]

Initial release

2021-04-30

sequoia

Functions (70)

sequoia

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