Taxonomic record dictionary

Taxonomic dictionary contains a taxonomic tree and NCBI taxonomy data for all taxonomic IDs.

Usage

# S4 method for TaxDict
as.character(x)

# S4 method for TaxDict
show(object)

# S4 method for TaxDict
print(x)

# S4 method for TaxDict
str(object, max.level = 2L, ...)

# S4 method for TaxDict
summary(object)

Arguments

x

TaxDict object

object

TaxDict object

max.level

Maximum level of nesting for str()

...

Further arguments for str()

Slots

txids

Taxonomic IDs of taxon records

recs

Environment of records

prnt

Parent taxonomic ID

txtr

Taxonomic tree

See also

Other run-public: ClstrArc-class, ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

data('aotus')
txdct <- aotus@txdct
# this is a TaxDict object
# it contains taxonomic information, including records and tree
show(txdct)
#> Taxonomic dictionary [22] recs, parent [id 9504]
# you can access its different data slots with @
txdct@txids  # taxonomic IDs
#>  [1] "2688256" "1263727" "1230482" "1090913" "1002694" "940829"  "867331" 
#>  [8] "413234"  "361674"  "292213"  "280755"  "261316"  "231953"  "222417" 
#> [15] "120088"  "57176"   "57175"   "43147"   "37293"   "30591"   "9505"   
#> [22] "9504"   
txdct@recs   # taxonomic records environment
#> <environment: 0x5f6434498908>
txdct@txtr   # taxonomic tree
#> TreeMan Object of [19] tips
txdct@prnt   # MRCA
#> [1] "9504"
# access any record through the records environment
txdct@recs[[txdct@txids[[1]]]]
#> TaxRec [id 2688256 (unclassified Aotus (in: primates))]
# for interacting with the taxonomic tree, see the treeman package
summary(txdct@txtr)
#> Tree (TreeMan Object):
#>   + 19 tips
#>   + 3 internal nodes
#>   + Polytomous
#>   + PD 22
#>   + Root node is "9504"