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For all sequences in a cluster(s) calculate the frequency of separate words in either the sequence definitions or the reported feature name.

Usage

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().

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'))
#> $`221`
#>     aenea 
#> 0.1692308 
#> 
#> $`196`
#> wrds
#>      gene       28s   partial  sequence 
#> 0.1118881 0.1048951 0.1048951 0.1048951 
#> 
#> $`346`
#> named numeric(0)
#> 
#> $`607`
#> named numeric(0)
#> 
#> $`628`
#> named numeric(0)
#> 
#> $`232`
#> named numeric(0)
#> 
#> $`402`
#> named numeric(0)
#> 
#> $`699`
#> named numeric(0)
#> 
#> $`29`
#> named numeric(0)
#> 
#> $`448`
#> named numeric(0)
#> 
# most frequent words in feature name
(calc_wrdfrq(phylota = dragonflies, cid = random_cids, type = 'nm'))
#> $`221`
#> numeric(0)
#> 
#> $`196`
#> numeric(0)
#> 
#> $`346`
#> numeric(0)
#> 
#> $`607`
#> numeric(0)
#> 
#> $`628`
#> numeric(0)
#> 
#> $`232`
#> numeric(0)
#> 
#> $`402`
#> numeric(0)
#> 
#> $`699`
#> barcode 
#>       1 
#> 
#> $`29`
#> numeric(0)
#> 
#> $`448`
#> numeric(0)
#>