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sequoia (version 2.0.7)

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

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Version

Install

install.packages('sequoia')

Monthly Downloads

670

Version

2.0.7

License

GPL-2

Maintainer

Jisca Huisman

Last Published

May 18th, 2020

Functions in sequoia (2.0.7)

Simulate genotyping errors

Comparison of all pairwise relationships in 2 pedigrees

calculate OH and LLR

Assign family IDs

Extract sex and birthyear from PLINK file

Pairwise relationship

Estimate genotyping error rate

SNPs scored in both individuals

Example life history file

Convert genotype data

Find putative relatives

Plot age priors

Simulate genotyping errors

Inheritance patterns

Compare two Pedigrees

Example pedigree

SimGeno_example

Example genotype file

Example pedigree: griffins

SNP summary statistics

Assignability of reference pedigree

Example sequoia output (griffins)

Summarise sequoia output or pedigree

backtransform IDs

Compare two vectors

Simulated genotypes

Generate error matrix

Find the closest matching inferred sibship to a true sibship

Fortran wrapper for pedigree reconstruction

Count generations

Estimate confidence probability

write sequoia output to excel or text files

write data to a file column-wise

Order lifehistory data

Pedigree Reconstruction

Plot summary overview of sequoia output

CalcMaxMismatch

Maximum number of mismatches

Check data for duplicates.

Perform chi-square test on observed vs expected genotypes

check LifeHistData