sequoia3.0.3 package

Check LifeHistData

Check if input parameters are valid

Compare Pairwise Relationships

Tabulate Age Differences

Fortran Simulate Genotyping Errors

Make Pairs Fortran Compatible

Convert Genotype Data

Get ancestors

Estimate Genotyping Error Rate

Order Lifehistory Data

PARAM to Specs

Compare Two Pedigrees

Plot Summary Overview of sequoia Output

plot SnpStats results

Find siblings

select non-genotyped parents

Change Numeric Pedigree back to Character Pedigree

Square Venn diagram

Write Data to a File Column-wise

Birth year probabilities

Corner coordinates

Maximum Number of Mismatches

Calculate OH and LLR for a pedigree

Calculate Likelihoods for Alternative Relationships

Calculate Pedigree Relatedness

check AgePrior

Check Genotype Matrix

Check Data for Duplicates.

Compare Dyads (DEPRECATED)

Generate Genotyping Error Matrix

Confidence Probabilities

Estimate genotyping error rate (REMOVED; will be re-implemented)

Assign Family IDs

Fold IDs of Sibship Grandparents

Assignability of Reference Pedigree

Get descendants

Dummifiable IDs

Count Generations

LLR-age from Ageprior Matrix

Find Putative Relatives

Array with Pairwise Relationships

Matrix with Pairwise Relationships

Extract Sex and Birth Year from PLINK File

Scatter Plot of Pair LLRs

Age Priors

Special Merge

Make default 1/0 ageprior

PARAM to FortPARAM

Simulate Genotyping Errors

Check and recode mtSame matrix

Fix Pedigree

Back-transform IDs

Turn Character Pedigree into Numeric Pedigree

Plot Age Priors

Plot Pair Log10-Likelihoods

Visualise PedCompare Output

Plot Pairwise Relationships

Fortran Wrapper for Pedigree Reconstruction

Pedigree Reconstruction

Find the closest matching inferred sibship to a true sibship

Simulate Genotypes

Smooth out dips in ageprior matrix

SNP Summary Statistics

Specs to PARAM

Summarise Sequoia Output or Pedigree

tryCatch both warnings (with value) and errors

Compare two vectors

Write Sequoia Output to File