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sequoia (version 1.3.3)

Pedigree Inference from SNPs

Description

Fast 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, citation('sequoia')) for more information.

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Version

Install

install.packages('sequoia')

Monthly Downloads

670

Version

1.3.3

License

GPL-2

Maintainer

Jisca Huisman

Last Published

June 20th, 2019

Functions in sequoia (1.3.3)

MakeAgePrior

Age priors
PedCompare

Compare two Pedigrees
rc

Find siblings
SimGeno_example

Example genotype file
MkGenoErrors

Simulate genotyping errors
plot.seq

Plot summary overview of sequoia output
SimGeno

Simulated genotypes
SeqParSib

Fortran wrapper for pedigree reconstruction
Vcomp

Compare two vectors
PlotAgePrior

Plot age priors
MergeFill

special merge
PedStripFID

backtransform IDs
LH_HSg5

Example life history file
LHConvert

Extract sex and birthyear from PLINK file
WrapDup

Check data for duplicates.
SummarySeq

Summarise sequoia output or pedigree
SnpStats

SNP summary statistics
writeColumns

write data to a file column-wise
GetMaybeRel

Find putative relatives
SibMatch

Find the closest matching inferred sibship to a true sibship
sequoia

Pedigree Reconstruction
SeqPrep

preparations
Ped_HSg5

Example pedigree
orderLH

Order lifehistory data
getGenerations

Count generations
writeSeq

write sequoia output to excel or text files
EstConf

Estimate confidence probability
GenoConvert

Convert genotype data
DyadCompare

Compare dyads
DoErrors

Simulate genotyping errors
FindFamilies

Assign family IDs
GetRelCat

Pairwise relationship
CheckGeno

check GenoM
CheckLH

check LifeHistData
Inherit

Inheritance patterns