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sequoia (version 1.3.1)

Pedigree Inference from SNPs

Description

Fast multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See citation('sequoia') for more information.

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Version

Install

install.packages('sequoia')

Monthly Downloads

670

Version

1.3.1

License

GPL-2

Maintainer

Jisca Huisman

Last Published

June 14th, 2019

Functions in sequoia (1.3.1)

FindFamilies

Assign family IDs
Inherit

Inheritance patterns
DyadCompare

Compare dyads
GetMaybeRel

Find putative relatives
DoErrors

Simulate genotyping errors
GetRelCat

Pairwise relationship
EstConf

Estimate confidence probability
GenoConvert

Convert genotype data
CheckGeno

check GenoM
CheckLH

check LifeHistData
MkGenoErrors

Simulate genotyping errors
PedStripFID

backtransform IDs
PlotAgePrior

Plot age priors
Ped_HSg5

Example pedigree
Vcomp

Compare two vectors
SeqParSib

Fortran wrapper for pedigree reconstruction
PedCompare

Compare two Pedigrees
LHConvert

Extract sex and birthyear from PLINK file
LH_HSg5

Example life history file
orderLH

Order lifehistory data
getGenerations

Count generations
SnpStats

SNP summary statistics
SummarySeq

Summarise sequoia output or pedigree
writeSeq

write sequoia output to excel or text files
MergeFill

special merge
MakeAgePrior

Age priors
plot.seq

Plot summary overview of sequoia output
WrapDup

Check data for duplicates.
SeqPrep

preparations
rc

Find siblings
SibMatch

Find the closest matching inferred sibship to a true sibship
SimGeno

Simulated genotypes
sequoia

Pedigree Reconstruction
writeColumns

write data to a file column-wise
SimGeno_example

Example genotype file