Learn R Programming
⚠️There's a newer version (3.0.3) of this package.Take me there.

sequoia (version 2.11.2)

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.

Copy Link

Version

Install

install.packages('sequoia')

Monthly Downloads

813

Version

2.11.2

License

GPL-2

Maintainer

Jisca Huisman

Last Published

May 28th, 2024

Functions in sequoia (2.11.2)

CountAgeDif

Tabulate Age Differences
EstConf

Confidence Probabilities
ErrToM

Generate Genotyping Error Matrix
DyadCompare

Compare Dyads (DEPRECATED)
EstEr

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

Compare Pairwise Relationships
DoErrors

Fortran Simulate Genotyping Errors
DuplicateCheck

Check Data for Duplicates.
FieldMums_griffin

Example field-observed mothers: griffins
Conf_griffin

Example output from estimating confidence probabilities: griffins
FindFamilies

Assign Family IDs
GenoConvert

Convert Genotype Data
FortifyPairs

Make Pairs Fortran Compatible
FoldSibGPs

Fold IDs of Sibship Grandparents
GetLLRAge

LLR-age from Ageprior Matrix
GetAncestors

Get ancestors
GetDummifiable

Dummifiable IDs
Geno_HSg5

Example genotype file: 'HSg5'
GetDescendants

Get descendants
LH_HSg5

Example life history file: 'HSg5'
LHConvert

Extract Sex and Birth Year from PLINK File
GetMaybeRel

Find Putative Relatives
MakeAgePrior

Age Priors
GetRelM

Matrix with Pairwise Relationships
LLRplot

Scatter Plot of Pair LLRs
GetRelA

Array with Pairwise Relationships
Geno_griffin

Example genotype file: Griffins
MaybeRel_griffin

Example output from check for relatives: griffins
LH_griffin

Example life history data: griffins
Inherit_patterns

Inheritance patterns
MkGenoErrors

Simulate Genotyping Errors
PedPolish

Fix Pedigree
PedStripFID

Back-transform IDs
PedCompare

Compare Two Pedigrees
NumToID

Change Numeric Pedigree back to Character Pedigree
OHperSNP

Estimate Genotyping Error Rate
MkAPdefault

Make default 1/0 ageprior
MkFortParams

PARAM to FortPARAM
ParamToSpecs

PARAM to Specs
MergeFill

Special Merge
PlotRelPairs

Plot Pairwise Relationships
PlotSnpStats

plot SnpStats results
PlotAgePrior

Plot Age Priors
PlotPedComp

Visualise PedCompare Output
PlotPairLL

Plot Pair Log10-Likelihoods
Ped_griffin

Example pedigree: griffins
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
SpecsToParam

Specs to PARAM
PedToNum

Turn Character Pedigree into Numeric Pedigree
PlotSeqSum

Plot Summary Overview of sequoia Output
SelectNotSampled

select non-genotyped parents
SimGeno

Simulate Genotypes
SummarySeq

Summarise Sequoia Output or Pedigree
Ped_HSg5

Example pedigree: 'HSg5'
SeqOUT_HSg5

Example output from pedigree inference: 'HSg5'
SibMatch

Find the closest matching inferred sibship to a true sibship
SmoothAP

Smooth out dips in ageprior matrix
getAssignCat

Assignability of Reference Pedigree
SeqOUT_griffin

Example output from pedigree inference: griffins
SimGeno_example

Example genotype file: 'HSg5'
SnpStats

SNP Summary Statistics
getGenerations

Count Generations
tryCatch.W.E

tryCatch both warnings (with value) and errors
writeColumns

Write Data to a File Column-wise
VennSquares

Square Venn diagram
Vcomp

Compare two vectors
writeSeq

Write Sequoia Output to File
sequoia

Pedigree Reconstruction
rc

Find siblings
mtSame2Dif

Check and recode mtSame matrix
orderLH

Order Lifehistory Data
CheckLH

Check LifeHistData
CalcBYprobs

Birth year probabilities
CheckAP

check AgePrior
CalcRped

Calculate Pedigree Relatedness
CheckGeno

Check Genotype Matrix
CheckParams

Check if input parameters are valid
CalcMaxMismatch

Maximum Number of Mismatches
CalcCorners

Corner coordinates
CalcOHLLR

Calculate OH and LLR for a pedigree
CalcPairLL

Calculate Likelihoods for Alternative Relationships