sequoia3.1.3 package

Calculate Likelihoods for Alternative Relationships

Calculate assignment probabilities

Calculate Pedigree Relatedness

check AgePrior

Check Genotype Matrix

Check LifeHistData

Check if input parameters are valid

Compare Pairwise Relationships

Estimate Genotyping Error Rate

Order Lifehistory Data

PARAM to Specs

Compare Two Pedigrees

Plot proportion of individuals that has a parent assigned

Plot Pairwise Relationships

Plot Summary Overview of sequoia Output

plot SnpStats results

Find siblings

Re-order likelihood vector

select non-genotyped parents

Square Venn diagram

Write Data to a File Column-wise

Maximum Number of Mismatches

Calculate OH and LLR for a pedigree

Birth year probabilities

Corner coordinates

Count opposing homozygous SNPs between pairs of individuals

Fortran Simulate Genotyping Errors

Check Data for Duplicates.

Compare Dyads (DEPRECATED)

Convert Genotyping Error Rates from per-allele to per-locus

Generate Genotyping Error Matrix

Confidence Probabilities

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

Assign Family IDs

Fold IDs of Sibship Grandparents

Make Pairs Fortran Compatible

Convert Genotype Data

Get ancestors

Simulate Genotyping Errors

Assignability of Reference Pedigree

Get descendants

Count Generations

LLR-age from Ageprior Matrix

Find Putative Relatives

Array with Pairwise Relationships

Matrix with Pairwise Relationships

Check and recode mtSame matrix

Extract Sex and Birth Year from PLINK File

Scatter Plot of Pair LLRs

transform log-likelihoods to probabilities

Age Priors

Special Merge

Make default 1/0 ageprior

PARAM to FortPARAM

Change Numeric Pedigree back to Character Pedigree

Fix Pedigree

Back-transform IDs

Turn Character Pedigree into Numeric Pedigree

Plot Age Priors

Plot Pair Log10-Likelihoods

Visualise PedCompare Output

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