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sequoia (version 2.3.5)

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

2.3.5

License

GPL-2

Maintainer

Jisca Huisman

Last Published

May 22nd, 2021

Functions in sequoia (2.3.5)

CalcRped

Calculate Pedigree Relatedness
CalcOHLLR

Calculate OH and LLR
CheckGeno

Check Genotype Matrix
CalcChi2

Chi-square Test on Observed vs Expected Genotypes
CalcBYprobs

Birth year probabilities
CalcMaxMismatch

Maximum Number of Mismatches
CalcPairLL

Calculate Likelihoods for Alternative Relationships
CalcCorners

Corner coordinates
CheckLH

Check LifeHistData
CheckAP

check AgePrior
ErrToM

Generate Genotyping Error Matrix
EstConf

Confidence Probabilities
Inherit

Inheritance patterns
GetRelM

Matrix with Pairwise Relationships
GetLLRAge

LLR-age from Ageprior Matrix
GetDummifiable

Dummifiable IDs
ComparePairs

Compare Pairwise Relationships
CheckParams

Check if input parameters are valid
FindFamilies

Assign Family IDs
FoldSibGPs

Fold IDs of Sibship Grandparents
NumToID

Change Numeric Pedigree back to Character Pedigree
ParamToSpecs

PARAM to Specs
DyadCompare

Compare Dyads
LH_griffin

Example lifehistory data: griffins
MkGenoErrors

Simulate Genotyping Errors
GetMaybeRel

Find Putative Relatives
MakeAgePrior

Age Priors
DoErrors

Fortran Simulate Genotyping Errors
CountAgeDif

Tabulate Age Differences
DuplicateCheck

Check Data for Duplicates.
MkFortParams

PARAM to FortPARAM
GetRelA

Array with Pairwise Relationships
Ped_HSg5

Example pedigree
PlotPedComp

Visualise PedCompare Output
Ped_griffin

Example pedigree: griffins
PedStripFID

Back-transform IDs
MergeFill

Special Merge
SnpStats

SNP Summary Statistics
plot.seq

Plot Summary Overview of sequoia Output
rc

Find siblings
PedToNum

Turn Character Pedigree into Numeric Pedigree
PedCompare

Compare Two Pedigrees
SimGeno_example

Example genotype file
PlotRelPairs

Plot Pairwise Relationships
EstErr

Estimate Genotyping Error Rate
LLRplot

Scatter Plot of Pair LLRs
Vcomp

Compare two vectors
sequoia

Pedigree Reconstruction
PedPolish

Fix Pedigree
FieldMums_griffin

Example field-observed mothers: griffins
GenoConvert

Convert Genotype Data
VennSquares

Square Venn diagram
FortifyPairs

Make Pairs Fortran Compatible
getAssignCat

Assignability of Reference Pedigree
SeqOUT_griffin

Example sequoia output (griffins)
getGDO

get individual category: genotyped, dummy, observed
PlotPairLL

Plot Pair Log10-Likelihoods
PlotAgePrior

Plot Age Priors
LHConvert

Extract Sex and Birth Year from PLINK File
SibMatch

Find the closest matching inferred sibship to a true sibship
SimGeno

Simulate Genotypes
getGenerations

Count Generations
LH_HSg5

Example life history file
SeqParSib

Fortran Wrapper for Pedigree Reconstruction
tryCatch.W.E

tryCatch both warnings (with value) and errors
orderLH

Order Lifehistory Data
SummarySeq

Summarise Sequoia Output or Pedigree
writeColumns

Write Data to a File Column-wise
writeSeq

Write Sequoia Output to File
SpecsToParam

Specs to PARAM