Man pages for sequoia
Pedigree Inference from SNPs
| CalcBYprobs | Birth year probabilities |
| CalcCorners | Corner coordinates |
| CalcMaxMismatch | Maximum Number of Mismatches |
| CalcOHLLR | Calculate OH and LLR for a pedigree |
| CalcPairLL | Calculate Likelihoods for Alternative Relationships |
| CalcParentProbs | Calculate assignment probabilities |
| CalcRped | Calculate Pedigree Relatedness |
| CheckAP | check AgePrior |
| CheckGeno | Check Genotype Matrix |
| CheckLH | Check LifeHistData |
| CheckParams | Check if input parameters are valid |
| ComparePairs | Compare Pairwise Relationships |
| Conf_griffin | Example output from estimating confidence probabilities:... |
| DoErrors | Fortran Simulate Genotyping Errors |
| DuplicateCheck | Check Data for Duplicates. |
| DyadCompare | Compare Dyads (DEPRECATED) |
| Err_RADseq | Convert Genotyping Error Rates from per-allele to per-locus |
| ErrToM | Generate Genotyping Error Matrix |
| EstConf | Confidence Probabilities |
| EstEr | Estimate genotyping error rate (REMOVED; will be... |
| FieldMums_griffin | Example field-observed mothers: griffins |
| FindFamilies | Assign Family IDs |
| FoldSibGPs | Fold IDs of Sibship Grandparents |
| FortifyPairs | Make Pairs Fortran Compatible |
| GenoConvert | Convert Genotype Data |
| Geno_griffin | Example genotype file: Griffins |
| Geno_HSg5 | Example genotype file: 'HSg5' |
| GetAncestors | Get ancestors |
| getAssignCat | Assignability of Reference Pedigree |
| GetDescendants | Get descendants |
| getGenerations | Count Generations |
| GetLLRAge | LLR-age from Ageprior Matrix |
| GetMaybeRel | Find Putative Relatives |
| GetRelA | Array with Pairwise Relationships |
| GetRelM | Matrix with Pairwise Relationships |
| Inherit_patterns | Inheritance patterns |
| LHConvert | Extract Sex and Birth Year from PLINK File |
| LH_griffin | Example life history data: griffins |
| LH_HSg5 | Example life history file: 'HSg5' |
| LLRplot | Scatter Plot of Pair LLRs |
| LLtoProb | transform log-likelihoods to probabilities |
| MakeAgePrior | Age Priors |
| MaybeRel_griffin | Example output from check for relatives: griffins |
| MergeFill | Special Merge |
| MkAPdefault | Make default 1/0 ageprior |
| MkFortParams | PARAM to FortPARAM |
| MkGenoErrors | Simulate Genotyping Errors |
| mtSame2Dif | Check and recode mtSame matrix |
| NumToID | Change Numeric Pedigree back to Character Pedigree |
| OHperSNP | Estimate Genotyping Error Rate |
| orderLH | Order Lifehistory Data |
| ParamToSpecs | PARAM to Specs |
| PedCompare | Compare Two Pedigrees |
| Ped_griffin | Example pedigree: griffins |
| Ped_HSg5 | Example pedigree: 'HSg5' |
| PedPolish | Fix Pedigree |
| PedStripFID | Back-transform IDs |
| PedToNum | Turn Character Pedigree into Numeric Pedigree |
| PlotAgePrior | Plot Age Priors |
| PlotPairLL | Plot Pair Log10-Likelihoods |
| PlotPedComp | Visualise PedCompare Output |
| PlotRelPairs | Plot Pairwise Relationships |
| PlotSeqSum | Plot Summary Overview of sequoia Output |
| PlotSnpStats | plot SnpStats results |
| rc | Find siblings |
| ReOrderDums | Re-order likelihood vector |
| SelectNotSampled | select non-genotyped parents |
| SeqOUT_griffin | Example output from pedigree inference: griffins |
| SeqOUT_HSg5 | Example output from pedigree inference: 'HSg5' |
| SeqParSib | Fortran Wrapper for Pedigree Reconstruction |
| sequoia | Pedigree Reconstruction |
| SibMatch | Find the closest matching inferred sibship to a true sibship |
| SimGeno | Simulate Genotypes |
| SimGeno_example | Example genotype file: 'HSg5' |
| SmoothAP | Smooth out dips in ageprior matrix |
| SnpStats | SNP Summary Statistics |
| SpecsToParam | Specs to PARAM |
| SummarySeq | Summarise Sequoia Output or Pedigree |
| tryCatch.W.E | tryCatch both warnings (with value) and errors |
| Vcomp | Compare two vectors |
| VennSquares | Square Venn diagram |
| writeColumns | Write Data to a File Column-wise |
| writeSeq | Write Sequoia Output to File |
