Description Usage Arguments Details Value See Also Examples
View source: R/construct_ngrams.R
Builds and selects important ngrams stepwise.
1 2 3 4 5 6 7 8 9  construct_ngrams(
target,
seq,
u,
n_max,
conf_level = 0.95,
gap = TRUE,
use_heuristics = TRUE
)

target 

seq 
a vector or matrix describing sequence(s). 
u 

n_max 
size of constructed ngrams. 
conf_level 
confidence level. 
gap 

use_heuristics, 
if 
construct_ngrams
starts by
extracting unigrams from the sequences, pasting them together in all combination and
choosing from them significant features (with pvalue below conf_level
). The
chosen ngrams are further extended to the specified by n_max
size by pasting
unigrams at both ends.
The gap
parameter determines if construct_ngrams
performs the
feature selection on exact ngrams (gap
equal to FALSE) or on all features in the
Hamming distance 1 from the ngram (gap
equal to TRUE).
a vector of ngrams.
Feature filtering method: test_features
.
1 2 3 4 5 6 7 8 9  # to make the example faster, we run construct_ngrams() on the
# subset of data
deg_seqs < degenerate(human_cleave[c(1L:100, 801L:900), 1L:9],
list(`1` = c(1, 6, 8, 10, 11, 18),
`2` = c(2, 13, 14, 16, 17),
`3` = c(5, 19, 20),
`4` = c(7, 9, 12, 15),
'5' = c(3, 4)))
bigrams < construct_ngrams(human_cleave[c(1L:100, 801L:900), "tar"], deg_seqs, 1L:5, 2)

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