Man pages for Ahhgust/MMDIT
Mitochondrial mixture project
| addKnownHaplotypes | reads empop; adds haplotypes to database This function takes... |
| countTraversalsMissedNodes | For each set of traversals, will count the number of missed... |
| createPlafPan | A helper function to runDeploid()that creates panel and plaf... |
| Empop2variant | Get variants from an EMPOP file |
| enumerateTraversalPossibilities | Enumerate the possible sets of traversals. |
| estimateLog10LikelihoodNaive | Estimates a naive (frequency-based) log10-likelihood of a set... |
| estimateLog10LikelihoodTheta | Theta-corrected likelihood computation |
| estimateLogLikelihood | Multi-population log-likelihood estimation |
| estimateTheta | Estimates Fst and quantiles of Fst |
| expandTraversalEditSequence | Get the edit sequence a traversal represents. |
| expandTraversalGraphDifferences | Get the variations from the reference that a traversal... |
| findExplainingIndividuals | Find sets of individuals that can explain the graph. |
| fst_buckleton | Estimates theta |
| getAllDistances | generates amplicon sequence data from difference encodings |
| getAmpCoordinates | Get amplicon coordinates |
| getAmps | makes amps |
| getdEploidHaps | Get estimated haplotypes based on the dEploid output |
| getMitoGenomes | gets full mitogenomes |
| getMixProps | Get proportion of mixtures from dEploid output |
| getMtgenomeLength | Length of mito-genome (reference) |
| getMtgenomeSequence | Mito-genome (reference) sequence |
| getNN | finds nearest neighbors |
| getPops | gets population labels |
| getRefAmpSeqs | Amplicon sequences of reference |
| getSeqdiffs | get all seqdiffs for some population |
| getSeqdiffsByAmp | get all seqdiffs for some population |
| getTraversalEditDistances | Will return the edit distances for the possible alignments to... |
| getTraversalHitNodes | Will return the nodes in the graph that the selected... |
| getTraversalsEditDistances | Vectorized version of getTraversalEditDistances. |
| getTraversalsHitNodes | Will return the nodes in the graph that the selected... |
| harmonizeAR | A helper function to runDeploid()that harmonizes the AltRef |
| harmonizePa | A helper function to runDeploid()that harmonizes the panel |
| harmonizePl | A helper function to runDeploid()that harmonizes the plaf |
| Hmtdb2Empop | Join mutliple EMPOP files into one large EMPOP file using a... |
| ksw2_gg_align | Global alignment of 2 strings |
| listGraphNodes | Lists the nodes in a sequence graph. |
| loadMMDIT | Loads MMDIT |
| loadReferenceGenome | Use this to add the rCRS sequence to MMDIT It adds the record... |
| makeDB | Creates (an empty) MMDIT database |
| makeDeploidSeqGraph | seqgraphs! |
| makeVariantGraph | Given a description of the variants in a mixture, will... |
| MMDIT | MMDIT |
| naiveGetAllNN | solves the All 1NN |
| naiveGetAllNNBySampAndStop | solves the All 1NN |
| preprocessMitoGenomes | Preprocess mitochondrial genomes |
| rundEploid | Wrapper function for dEploid |
| semicontinuousWrapper | Semicontinuous LRs |
| seqdiffs2seq | Computes a string from a difference encoding |
| Snp2variant | Get variants from SNP data |
| str2int | strings to ints |
| threepersonMix | 3 person mixture simulations |
| traverseSequenceGraph | Will return all alignments of a sequence to a graph (within... |
| traverseSequencesGraph | Vectorized version of traverseSequenceGraph. |
| twopersonMix | 2 person mixture simulations |
| twopersonMixOriginal | 2 person mixture simulations |
| Variant2snp | Get SNPs from variant data |
| writeAmp | Writes amplicon data to MMDIT |
| write_mbop | Write inforatuon on sample ID and variants in the emp file... |
