Man pages for trvinh/taxFun
taxFun
| convert2id | Convert a list of input taxa into taxon IDs |
| convert2name | Convert a list of input taxa into taxon names |
| createTaxonomyMatrix | Create an aligned taxonomy matrix for a list of taxon IDs |
| createTree | Create taxonomy tree for a list of taxa |
| createTreeSlow | Create taxonomy tree for a list of taxa (slow version) |
| firstup | Capitalize the first character of string(s) |
| getAllTaxonomyRanks | Get all NCBI taxonomy rank names |
| getClade | Get subset of taxa that belong to a specified taxonomy clade |
| getHierarchy | Get taxonomy hierarchy string for a list of taxon IDs |
| getLCA | Get last common ancestor for a list of taxa |
| getPreTaxonomyFile | Get PhyloProfile taxonomy file if available or create one if... |
| getRank | Get taxonomy ranks for a list of taxa |
| getRanks | Get defined taxonomy ranks for a list of taxa |
| getRepresentative | Get representative from a list of taxa based on a selected... |
| id2name | Get taxon names for a list of taxon IDs |
| name2id | Get taxon IDs for a list of taxon names |
| predictType | Predict type (ID or NAME) for a list of input taxa |
| sortTaxonomyMatrix | Sort a taxonomy matrix based on a defined reference species |
| taxFun | Run taxFun |
