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sequoia (version 2.11.1)

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

752

Version

2.11.1

License

GPL-2

Maintainer

Jisca Huisman

Last Published

May 27th, 2024

Functions in sequoia (2.11.1)

CheckParams

Check if input parameters are valid
CalcMaxMismatch

Maximum Number of Mismatches
CheckGeno

Check Genotype Matrix
CheckLH

Check LifeHistData
CalcBYprobs

Birth year probabilities
CalcRped

Calculate Pedigree Relatedness
CalcOHLLR

Calculate OH and LLR for a pedigree
CalcPairLL

Calculate Likelihoods for Alternative Relationships
CalcCorners

Corner coordinates
CheckAP

check AgePrior
EstEr

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

Fortran Simulate Genotyping Errors
ErrToM

Generate Genotyping Error Matrix
CountAgeDif

Tabulate Age Differences
FieldMums_griffin

Example field-observed mothers: griffins
Conf_griffin

Example output from estimating confidence probabilities: griffins
ComparePairs

Compare Pairwise Relationships
EstConf

Confidence Probabilities
DyadCompare

Compare Dyads (DEPRECATED)
DuplicateCheck

Check Data for Duplicates.
GetDescendants

Get descendants
GetAncestors

Get ancestors
FindFamilies

Assign Family IDs
FortifyPairs

Make Pairs Fortran Compatible
FoldSibGPs

Fold IDs of Sibship Grandparents
GenoConvert

Convert Genotype Data
Geno_HSg5

Example genotype file: 'HSg5'
Geno_griffin

Example genotype file: Griffins
GetRelM

Matrix with Pairwise Relationships
GetDummifiable

Dummifiable IDs
LHConvert

Extract Sex and Birth Year from PLINK File
GetLLRAge

LLR-age from Ageprior Matrix
MakeAgePrior

Age Priors
Inherit_patterns

Inheritance patterns
LH_HSg5

Example life history file: 'HSg5'
MaybeRel_griffin

Example output from check for relatives: griffins
PedStripFID

Back-transform IDs
GetRelA

Array with Pairwise Relationships
PedPolish

Fix Pedigree
GetMaybeRel

Find Putative Relatives
MkGenoErrors

Simulate Genotyping Errors
ParamToSpecs

PARAM to Specs
MkFortParams

PARAM to FortPARAM
PedCompare

Compare Two Pedigrees
NumToID

Change Numeric Pedigree back to Character Pedigree
OHperSNP

Estimate Genotyping Error Rate
PedToNum

Turn Character Pedigree into Numeric Pedigree
Ped_HSg5

Example pedigree: 'HSg5'
LH_griffin

Example life history data: griffins
PlotAgePrior

Plot Age Priors
PlotRelPairs

Plot Pairwise Relationships
PlotSeqSum

Plot Summary Overview of sequoia Output
Ped_griffin

Example pedigree: griffins
SnpStats

SNP Summary Statistics
SmoothAP

Smooth out dips in ageprior matrix
SeqOUT_griffin

Example output from pedigree inference: griffins
SeqOUT_HSg5

Example output from pedigree inference: 'HSg5'
LLRplot

Scatter Plot of Pair LLRs
SpecsToParam

Specs to PARAM
SummarySeq

Summarise Sequoia Output or Pedigree
PlotSnpStats

plot SnpStats results
VennSquares

Square Venn diagram
tryCatch.W.E

tryCatch both warnings (with value) and errors
Vcomp

Compare two vectors
SelectNotSampled

select non-genotyped parents
writeColumns

Write Data to a File Column-wise
PlotPairLL

Plot Pair Log10-Likelihoods
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
PlotPedComp

Visualise PedCompare Output
SimGeno

Simulate Genotypes
SimGeno_example

Example genotype file: 'HSg5'
getAssignCat

Assignability of Reference Pedigree
MkAPdefault

Make default 1/0 ageprior
MergeFill

Special Merge
mtSame2Dif

Check and recode mtSame matrix
SibMatch

Find the closest matching inferred sibship to a true sibship
orderLH

Order Lifehistory Data
getGenerations

Count Generations
writeSeq

Write Sequoia Output to File
sequoia

Pedigree Reconstruction
rc

Find siblings