For all sequences in a cluster(s) calculate the frequency of separate words in either the sequence definitions or the reported feature name.
calc_wrdfrq(phylota, cid, min_frq = 0.1, min_nchar = 1, type = c("dfln", "nm"), ignr_pttrn = "[^a-z0-9]")
Arguments
| phylota | Phylota object |
|---|---|
| cid | Cluster ID(s) |
| min_frq | Minimum frequency |
| min_nchar | Minimum number of characters for a word |
| type | Definitions (dfln) or features (nm) |
| ignr_pttrn | Ignore pattern, REGEX for text to ignore. |
Value
list
Details
By default, anything that is not alphanumeric is ignored. 'dfln' and 'nm' match the slot names in a SeqRec, see list_seqrec_slots().
See also
Other tools-public: calc_mad,
drop_by_rank, drop_clstrs,
drop_sqs, get_clstr_slot,
get_nsqs, get_ntaxa,
get_sq_slot, get_stage_times,
get_tx_slot, get_txids,
is_txid_in_clstr,
is_txid_in_sq,
list_clstrrec_slots,
list_ncbi_ranks,
list_seqrec_slots,
list_taxrec_slots,
plot_phylota_pa,
plot_phylota_treemap,
read_phylota, write_sqs
Examples
data('dragonflies') # work out what gene region the cluster is likely representing with word freqs. random_cids <- sample(dragonflies@cids, 10) # most frequent words in definition line (calc_wrdfrq(phylota = dragonflies, cid = random_cids, type = 'dfln'))#> $`766` #> named numeric(0) #> #> $`535` #> named numeric(0) #> #> $`76` #> sequence #> 0.1245614 #> #> $`445` #> named numeric(0) #> #> $`566` #> named numeric(0) #> #> $`426` #> named numeric(0) #> #> $`61` #> named numeric(0) #> #> $`554` #> named numeric(0) #> #> $`772` #> wrds #> rrna and #> 0.1578947 0.1052632 #> #> $`468` #> named numeric(0) #># most frequent words in feature name (calc_wrdfrq(phylota = dragonflies, cid = random_cids, type = 'nm'))#> $`766` #> barcode #> 1 #> #> $`535` #> wrds #> rhswc1 rhswc2 rhswc3 rhswc4 rhswc5 #> 0.2 0.2 0.2 0.2 0.2 #> #> $`76` #> wrds #> internal spacer transcribed #> 0.3314286 0.3314286 0.3314286 #> #> $`445` #> numeric(0) #> #> $`566` #> coii #> 1 #> #> $`426` #> wrds #> rhlwc1 rhlwd1 rhlwe1 rhlwf1 rhlwf2 rhlwf3 rhlwf4 #> 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 #> #> $`61` #> co1 #> 1 #> #> $`554` #> numeric(0) #> #> $`772` #> wrds #> internal spacer transcribed #> 0.3333333 0.3333333 0.3333333 #> #> $`468` #> co1 #> 1 #>