Man pages for raim/ncbitax
Simple base R parser for NCBI Taxonomy
| edg2idx | convert edge table to named parent vector |
| getAllParents | get common parents for a list of taxon IDs |
| getAncestor | get lowest common ancestor |
| get.children | simple children retrieval |
| getChildren | get all chilrden of a node |
| getID | get taxon IDs from taxon names |
| getLineage | get NCBI taxonomy rank lineages |
| getName | gets taxon names from taxon IDs |
| get.parents | simple lineage retrieval |
| getParents | lineage retrieval |
| getRank | gets taxon ranks from taxon IDs |
| grepName | find taxon IDs for species name patterns |
| idx2edg | convert named parent vector to edge table |
| ncbitax | ncbitax: a simple NCBI taxonomy parser |
| parseNCBITaxonomy | load tbi taxonomy files |
| reduceTaxonomy | reduced taxonomy tree for faster searches |
| tax2newick | convert NCBI taxonomy sub trees to newick format |
| tax2phylo | converts an NCBI taxonomy object to an 'ape::phylo' tree |
| updateIDs | update a list of taxonomy IDs |
