dbTaxonomy: Read and Write Taxonomy Table
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Details Value See Also

Create, extend and read the taxonomy table of a megaptera project.

dbReadTaxonomy(
  megProj,
  tip.rank,
  subset,
  tag,
  root = "tol",
  syn = FALSE,
  drop.extinct = TRUE
)

dbUpdateTaxonomy(megProj, taxonomy, logfile = "")

`megProj`	An object of class `megapteraProj`.
`tip.rank`	A character string giving the rank of the tips (e.g. `species`, `genus`, ...).
`subset`	A subset of species names (Latin binomials) to which the taxonomy should be limited. Can be a DNA alignment of class `DNAbin`, a phylogenetic tree of class `phylo`,`species_sequence` (see Details), or a character vector.
`tag`	A character string used to tag the rows of `taxonomy` in the postgreSQL table; this argument is mostly for internal use.
`root`	A character string. By default (`"tol"`), all higher ranks from the most recent common ancestor (MRCA) of the clade of interest down to the root are included in the taxonomic classification, whereas `"mrca"` means that only the MRCA will be included. Note that this option only makes sense in combination with `subset`.
`syn`	Logical, indicating if synonyms should be returned in addition to accepted names.
`drop.extinct`	Logical, if `TRUE` all lineages that lack a taxon of rank `"tip.rank"` will be pruned from the taxonomy.
`taxonomy`	A data frame containing a taxonomic classification of the study species. It will replace any existing taxonomy in the database.
`logfile`	A character string giving the names of a potential logfile; no logfile is written if this argument is left empty.

If step stepF has been run, dbReadTaxonomy can be called with subset = "species_sequence". In that case all species names with sequence data for the current locus will be used for subsetting.

For dbReadTable an object of class "data.frame" holding the taxonomic classification of target species. dbUpdateTaxonomy is called only for its side effect creating and extending the taxonomy database table.

ncbiTaxonomy for retrieval of taxonomies from the taxonomy database at NCBI; findRoot returns the lowest common rank for taxonomies. dbReadDNA and dbWriteDNA to read and write DNA sequences.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.