Package: sequoia 2.11.2

Jisca Huisman

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.

Authors:Jisca Huisman [aut, cre]

sequoia_2.11.2.tar.gz
sequoia_2.11.2.tar.gz(r-4.5-noble)sequoia_2.11.2.tar.gz(r-4.4-noble)
sequoia.pdf |sequoia.html✨
sequoia/json (API)
NEWS

# Install 'sequoia' in R:

install.packages('sequoia', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

fortran– Runtime library for GNU Fortran applications

Datasets:

Conf_griffin - Example output from estimating confidence probabilities: griffins
FieldMums_griffin - Example field-observed mothers: griffins
Geno_HSg5 - Example genotype file: 'HSg5'
Geno_griffin - Example genotype file: Griffins
Inherit_patterns - Inheritance patterns
LH_HSg5 - Example life history file: 'HSg5'
LH_griffin - Example life history data: griffins
MaybeRel_griffin - Example output from check for relatives: griffins
Ped_HSg5 - Example pedigree: 'HSg5'
Ped_griffin - Example pedigree: griffins
SeqOUT_HSg5 - Example output from pedigree inference: 'HSg5'
SeqOUT_griffin - Example output from pedigree inference: griffins
SimGeno_example - Example genotype file: 'HSg5'

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.14 score 1 stars 77 scripts 929 downloads 37 exports 3 dependencies

Last updated 5 months agofrom:5e5d326363. Checks:OK: 1 WARNING: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-linux-x86_64	WARNING	Oct 26 2024

Exports:CalcBYprobs CalcMaxMismatch CalcOHLLR CalcPairLL CalcRped CheckGeno ComparePairs DyadCompare ErrToM EstConf EstEr FindFamilies GenoConvert GetAncestors getAssignCat GetDescendants getGenerations GetLLRAge GetMaybeRel GetRelM LHConvert MakeAgePrior MkGenoErrors PedCompare PedPolish PedStripFID PlotAgePrior PlotPairLL PlotPedComp PlotRelPairs PlotSeqSum sequoia SimGeno SnpStats SummarySeq writeColumns writeSeq

Dependencies:cli plyr Rcpp

Mitochondrial haplotypes

Rendered fromvignette_mtDNA.pdf.asisusingR.rsp::asison Oct 26 2024.

Last update: 2024-05-28
Started: 2023-09-06

PedCompare Example (Griffin Pedigree)

Jisca Huisman ( jisca.huisman @ gmail.com )

Rendered fromPedComp.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-05-28
Started: 2021-04-29

Quick start example 1: Simulated data

J Huisman

Rendered fromquick_start_example1.rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-05-28
Started: 2021-04-29

Sequoia - Age 'Prior'

Jisca Huisman

Rendered fromvignette-age.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-05-28
Started: 2021-04-29

Sequoia flowchart

Rendered fromflowchart.pdf.asisusingR.rsp::asison Oct 26 2024.

Last update: 2024-05-28
Started: 2021-04-29

Sequoia User Guide

Jisca Huisman ( jisca.huisman @ gmail.com )

Rendered fromvignette-main.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-05-28
Started: 2021-04-29

Citation

Readme and manuals

Help Manual

Help page	Topics
Birth year probabilities	CalcBYprobs
Maximum Number of Mismatches	CalcMaxMismatch
Calculate OH and LLR for a pedigree	CalcOHLLR
Calculate Likelihoods for Alternative Relationships	CalcPairLL
Calculate Pedigree Relatedness	CalcRped
Check Genotype Matrix	CheckGeno
Compare Pairwise Relationships	ComparePairs
Example output from estimating confidence probabilities: griffins	Conf_griffin
Compare Dyads (DEPRECATED)	DyadCompare
Generate Genotyping Error Matrix	ErrToM
Confidence Probabilities	EstConf
Estimate genotyping error rate (REMOVED; will be re-implemented)	EstEr
Example field-observed mothers: griffins	FieldMums_griffin
Assign Family IDs	FindFamilies
Example genotype file: Griffins	Geno_griffin
Example genotype file: 'HSg5'	Geno_HSg5
Convert Genotype Data	GenoConvert
Get ancestors	GetAncestors
Assignability of Reference Pedigree	getAssignCat
Get descendants	GetDescendants
Count Generations	getGenerations
LLR-age from Ageprior Matrix	GetLLRAge
Find Putative Relatives	GetMaybeRel
Matrix with Pairwise Relationships	GetRelM
Inheritance patterns	Inherit_patterns
Example life history data: griffins	LH_griffin
Example life history file: 'HSg5'	LH_HSg5
Extract Sex and Birth Year from PLINK File	LHConvert
Age Priors	MakeAgePrior
Example output from check for relatives: griffins	MaybeRel_griffin
Simulate Genotyping Errors	MkGenoErrors
Example pedigree: griffins	Ped_griffin
Example pedigree: 'HSg5'	Ped_HSg5
Compare Two Pedigrees	PedCompare
Fix Pedigree	PedPolish
Back-transform IDs	PedStripFID
Plot Age Priors	PlotAgePrior
Plot Pair Log10-Likelihoods	PlotPairLL
Visualise PedCompare Output	PlotPedComp
Plot Pairwise Relationships	PlotRelPairs
Plot Summary Overview of sequoia Output	PlotSeqSum
Example output from pedigree inference: griffins	SeqOUT_griffin
Example output from pedigree inference: 'HSg5'	SeqOUT_HSg5
Pedigree Reconstruction	sequoia
Simulate Genotypes	SimGeno
Example genotype file: 'HSg5'	SimGeno_example
SNP Summary Statistics	SnpStats
Summarise Sequoia Output or Pedigree	SummarySeq
Write Data to a File Column-wise	writeColumns
Write Sequoia Output to File	writeSeq

Usage by other packages (reverse dependencies)