Man pages for CMWbio/geaR
GDS Evolutionary Analysis in R
| analyzeCog-methods | analyze cogs |
| analyzeGear-methods | analyzeGear |
| buildCodonDB-methods | build a codon sqlLite DB |
| cog-class | Cog classes |
| dmax | Calculates maximum genetic distance |
| dmin | Calculates minimum genetic distance |
| dxyAF | #' Calculates geentic distance between populations using... |
| filterCodonDB | filter codon position and type |
| gear-class | The gear Object Class |
| genoDist | Calculates the hamming distance between alleles |
| getAdmixFromGear | getAdmixFromGear |
| getAF | Calculates population based allele frequency |
| getCodonsFromFasta | get codon positions from fasta |
| getDivFromGear | getDivFromGear |
| getGenotypes | Import genotypes from GDS |
| getPositionFromDB-methods | getPositionFromDB |
| Gmin | Gmin |
| makeCogs-methods | Make cogs |
| makeFeatures-methods | getFeatures |
| makeGear | make gear object |
| mergeLoci | Combines overlaps in ys and xs |
| Nei82Fst | Fst from hamming distance |
| neisDa | Calculates Nei's ancestral/net genetic distance |
| neisDxy | Calculates Nei's Dxy |
| neisPi | Calculates Nei's nucleotide diversity (pi) |
| relDxy | Calculates Relative genetic distance (dxy) |
| RND | Calculates Relative Node Depth |
| snpWindowMaker-methods | Sliding or Tiled snpwindow maker. |
| summarizeStats | Calculates block jackknifed mean for statistics |
| validate4FoldCodons | Validate 4fold degenerate codons |
| windowMaker-methods | Sliding or Tiled window maker. |
