Extracts vector of n-grams present in sequence(s).

seq2ngrams(seq, n, u, d = 0, pos = FALSE)

Arguments

seq

a vector or matrix describing sequence(s).

n

integer size of n-gram.

u

integer, numeric or character vector of all possible unigrams.

d

integer vector of distances between elements of n-gram (0 means consecutive elements). See Details.

pos

logical, if TRUE position-specific n_grams are counted.

Value

A character matrix of n-grams, where every row corresponds to a different sequence.

Details

A format of d vector is discussed in Details of count_ngrams.

Examples

# trigrams from multiple sequences seqs <- matrix(sample(1L:4, 600, replace = TRUE), ncol = 50) seq2ngrams(seqs, 3, 1L:4)
#> [,1] [,2] [,3] [,4] [,5] [,6] #> [1,] "4.1.1_0.0" "1.1.1_0.0" "1.1.4_0.0" "1.4.2_0.0" "4.2.3_0.0" "2.3.3_0.0" #> [2,] "2.3.4_0.0" "3.4.2_0.0" "4.2.3_0.0" "2.3.4_0.0" "3.4.1_0.0" "4.1.2_0.0" #> [3,] "3.2.1_0.0" "2.1.3_0.0" "1.3.4_0.0" "3.4.1_0.0" "4.1.3_0.0" "1.3.1_0.0" #> [4,] "4.4.3_0.0" "4.3.3_0.0" "3.3.4_0.0" "3.4.1_0.0" "4.1.4_0.0" "1.4.1_0.0" #> [5,] "1.1.3_0.0" "1.3.4_0.0" "3.4.4_0.0" "4.4.2_0.0" "4.2.1_0.0" "2.1.1_0.0" #> [6,] "1.2.3_0.0" "2.3.2_0.0" "3.2.2_0.0" "2.2.4_0.0" "2.4.2_0.0" "4.2.4_0.0" #> [7,] "3.4.2_0.0" "4.2.4_0.0" "2.4.4_0.0" "4.4.2_0.0" "4.2.3_0.0" "2.3.2_0.0" #> [8,] "1.4.4_0.0" "4.4.3_0.0" "4.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.3_0.0" #> [9,] "2.3.1_0.0" "3.1.1_0.0" "1.1.4_0.0" "1.4.1_0.0" "4.1.1_0.0" "1.1.3_0.0" #> [10,] "2.4.4_0.0" "4.4.3_0.0" "4.3.1_0.0" "3.1.4_0.0" "1.4.1_0.0" "4.1.4_0.0" #> [11,] "4.2.3_0.0" "2.3.1_0.0" "3.1.2_0.0" "1.2.4_0.0" "2.4.1_0.0" "4.1.2_0.0" #> [12,] "1.4.1_0.0" "4.1.3_0.0" "1.3.1_0.0" "3.1.1_0.0" "1.1.4_0.0" "1.4.1_0.0" #> [,7] [,8] [,9] [,10] [,11] [,12] #> [1,] "3.3.2_0.0" "3.2.3_0.0" "2.3.2_0.0" "3.2.2_0.0" "2.2.3_0.0" "2.3.3_0.0" #> [2,] "1.2.1_0.0" "2.1.2_0.0" "1.2.2_0.0" "2.2.1_0.0" "2.1.1_0.0" "1.1.3_0.0" #> [3,] "3.1.3_0.0" "1.3.1_0.0" "3.1.1_0.0" "1.1.2_0.0" "1.2.4_0.0" "2.4.2_0.0" #> [4,] "4.1.2_0.0" "1.2.2_0.0" "2.2.1_0.0" "2.1.4_0.0" "1.4.3_0.0" "4.3.3_0.0" #> [5,] "1.1.3_0.0" "1.3.4_0.0" "3.4.1_0.0" "4.1.2_0.0" "1.2.2_0.0" "2.2.4_0.0" #> [6,] "2.4.1_0.0" "4.1.2_0.0" "1.2.2_0.0" "2.2.3_0.0" "2.3.3_0.0" "3.3.2_0.0" #> [7,] "3.2.2_0.0" "2.2.2_0.0" "2.2.4_0.0" "2.4.2_0.0" "4.2.3_0.0" "2.3.2_0.0" #> [8,] "1.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.2_0.0" "1.2.1_0.0" "2.1.2_0.0" #> [9,] "1.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.4_0.0" "1.4.3_0.0" "4.3.4_0.0" #> [10,] "1.4.4_0.0" "4.4.3_0.0" "4.3.2_0.0" "3.2.2_0.0" "2.2.4_0.0" "2.4.3_0.0" #> [11,] "1.2.4_0.0" "2.4.4_0.0" "4.4.2_0.0" "4.2.2_0.0" "2.2.2_0.0" "2.2.1_0.0" #> [12,] "4.1.4_0.0" "1.4.2_0.0" "4.2.4_0.0" "2.4.1_0.0" "4.1.1_0.0" "1.1.1_0.0" #> [,13] [,14] [,15] [,16] [,17] [,18] #> [1,] "3.3.3_0.0" "3.3.3_0.0" "3.3.4_0.0" "3.4.1_0.0" "4.1.2_0.0" "1.2.1_0.0" #> [2,] "1.3.1_0.0" "3.1.3_0.0" "1.3.2_0.0" "3.2.3_0.0" "2.3.2_0.0" "3.2.2_0.0" #> [3,] "4.2.4_0.0" "2.4.4_0.0" "4.4.3_0.0" "4.3.2_0.0" "3.2.3_0.0" "2.3.2_0.0" #> [4,] "3.3.4_0.0" "3.4.1_0.0" "4.1.2_0.0" "1.2.2_0.0" "2.2.3_0.0" "2.3.4_0.0" #> [5,] "2.4.1_0.0" "4.1.4_0.0" "1.4.2_0.0" "4.2.4_0.0" "2.4.3_0.0" "4.3.2_0.0" #> [6,] "3.2.1_0.0" "2.1.1_0.0" "1.1.4_0.0" "1.4.2_0.0" "4.2.4_0.0" "2.4.1_0.0" #> [7,] "3.2.4_0.0" "2.4.3_0.0" "4.3.1_0.0" "3.1.3_0.0" "1.3.1_0.0" "3.1.1_0.0" #> [8,] "1.2.2_0.0" "2.2.1_0.0" "2.1.2_0.0" "1.2.3_0.0" "2.3.1_0.0" "3.1.2_0.0" #> [9,] "3.4.3_0.0" "4.3.4_0.0" "3.4.3_0.0" "4.3.2_0.0" "3.2.2_0.0" "2.2.2_0.0" #> [10,] "4.3.1_0.0" "3.1.1_0.0" "1.1.4_0.0" "1.4.1_0.0" "4.1.3_0.0" "1.3.2_0.0" #> [11,] "2.1.1_0.0" "1.1.4_0.0" "1.4.1_0.0" "4.1.3_0.0" "1.3.4_0.0" "3.4.4_0.0" #> [12,] "1.1.1_0.0" "1.1.2_0.0" "1.2.3_0.0" "2.3.2_0.0" "3.2.4_0.0" "2.4.2_0.0" #> [,19] [,20] [,21] [,22] [,23] [,24] #> [1,] "2.1.1_0.0" "1.1.2_0.0" "1.2.3_0.0" "2.3.3_0.0" "3.3.1_0.0" "3.1.2_0.0" #> [2,] "2.2.2_0.0" "2.2.1_0.0" "2.1.4_0.0" "1.4.3_0.0" "4.3.2_0.0" "3.2.4_0.0" #> [3,] "3.2.4_0.0" "2.4.1_0.0" "4.1.3_0.0" "1.3.1_0.0" "3.1.1_0.0" "1.1.3_0.0" #> [4,] "3.4.3_0.0" "4.3.4_0.0" "3.4.1_0.0" "4.1.3_0.0" "1.3.1_0.0" "3.1.2_0.0" #> [5,] "3.2.3_0.0" "2.3.3_0.0" "3.3.3_0.0" "3.3.4_0.0" "3.4.3_0.0" "4.3.2_0.0" #> [6,] "4.1.3_0.0" "1.3.3_0.0" "3.3.3_0.0" "3.3.4_0.0" "3.4.2_0.0" "4.2.2_0.0" #> [7,] "1.1.3_0.0" "1.3.4_0.0" "3.4.1_0.0" "4.1.1_0.0" "1.1.2_0.0" "1.2.3_0.0" #> [8,] "1.2.3_0.0" "2.3.4_0.0" "3.4.4_0.0" "4.4.3_0.0" "4.3.4_0.0" "3.4.4_0.0" #> [9,] "2.2.2_0.0" "2.2.3_0.0" "2.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.1_0.0" #> [10,] "3.2.3_0.0" "2.3.3_0.0" "3.3.2_0.0" "3.2.3_0.0" "2.3.4_0.0" "3.4.1_0.0" #> [11,] "4.4.1_0.0" "4.1.3_0.0" "1.3.4_0.0" "3.4.1_0.0" "4.1.1_0.0" "1.1.4_0.0" #> [12,] "4.2.2_0.0" "2.2.2_0.0" "2.2.2_0.0" "2.2.3_0.0" "2.3.1_0.0" "3.1.4_0.0" #> [,25] [,26] [,27] [,28] [,29] [,30] #> [1,] "1.2.3_0.0" "2.3.2_0.0" "3.2.2_0.0" "2.2.1_0.0" "2.1.1_0.0" "1.1.4_0.0" #> [2,] "2.4.2_0.0" "4.2.1_0.0" "2.1.2_0.0" "1.2.2_0.0" "2.2.3_0.0" "2.3.1_0.0" #> [3,] "1.3.4_0.0" "3.4.4_0.0" "4.4.4_0.0" "4.4.4_0.0" "4.4.4_0.0" "4.4.1_0.0" #> [4,] "1.2.2_0.0" "2.2.1_0.0" "2.1.2_0.0" "1.2.2_0.0" "2.2.3_0.0" "2.3.2_0.0" #> [5,] "3.2.1_0.0" "2.1.2_0.0" "1.2.1_0.0" "2.1.3_0.0" "1.3.2_0.0" "3.2.1_0.0" #> [6,] "2.2.4_0.0" "2.4.4_0.0" "4.4.4_0.0" "4.4.4_0.0" "4.4.2_0.0" "4.2.4_0.0" #> [7,] "2.3.1_0.0" "3.1.1_0.0" "1.1.1_0.0" "1.1.1_0.0" "1.1.4_0.0" "1.4.4_0.0" #> [8,] "4.4.2_0.0" "4.2.4_0.0" "2.4.4_0.0" "4.4.2_0.0" "4.2.4_0.0" "2.4.3_0.0" #> [9,] "1.1.4_0.0" "1.4.4_0.0" "4.4.3_0.0" "4.3.1_0.0" "3.1.2_0.0" "1.2.3_0.0" #> [10,] "4.1.1_0.0" "1.1.1_0.0" "1.1.2_0.0" "1.2.4_0.0" "2.4.4_0.0" "4.4.4_0.0" #> [11,] "1.4.3_0.0" "4.3.4_0.0" "3.4.1_0.0" "4.1.4_0.0" "1.4.1_0.0" "4.1.4_0.0" #> [12,] "1.4.4_0.0" "4.4.3_0.0" "4.3.1_0.0" "3.1.3_0.0" "1.3.4_0.0" "3.4.2_0.0" #> [,31] [,32] [,33] [,34] [,35] [,36] #> [1,] "1.4.2_0.0" "4.2.4_0.0" "2.4.3_0.0" "4.3.1_0.0" "3.1.2_0.0" "1.2.2_0.0" #> [2,] "3.1.4_0.0" "1.4.4_0.0" "4.4.2_0.0" "4.2.4_0.0" "2.4.3_0.0" "4.3.1_0.0" #> [3,] "4.1.4_0.0" "1.4.3_0.0" "4.3.2_0.0" "3.2.2_0.0" "2.2.1_0.0" "2.1.2_0.0" #> [4,] "3.2.3_0.0" "2.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.2_0.0" "1.2.1_0.0" #> [5,] "2.1.3_0.0" "1.3.2_0.0" "3.2.3_0.0" "2.3.2_0.0" "3.2.3_0.0" "2.3.4_0.0" #> [6,] "2.4.1_0.0" "4.1.1_0.0" "1.1.1_0.0" "1.1.2_0.0" "1.2.1_0.0" "2.1.4_0.0" #> [7,] "4.4.3_0.0" "4.3.1_0.0" "3.1.2_0.0" "1.2.2_0.0" "2.2.1_0.0" "2.1.1_0.0" #> [8,] "4.3.3_0.0" "3.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.4_0.0" "1.4.2_0.0" #> [9,] "2.3.1_0.0" "3.1.4_0.0" "1.4.3_0.0" "4.3.1_0.0" "3.1.4_0.0" "1.4.2_0.0" #> [10,] "4.4.2_0.0" "4.2.3_0.0" "2.3.2_0.0" "3.2.3_0.0" "2.3.1_0.0" "3.1.2_0.0" #> [11,] "1.4.4_0.0" "4.4.1_0.0" "4.1.3_0.0" "1.3.1_0.0" "3.1.4_0.0" "1.4.2_0.0" #> [12,] "4.2.1_0.0" "2.1.4_0.0" "1.4.1_0.0" "4.1.2_0.0" "1.2.3_0.0" "2.3.1_0.0" #> [,37] [,38] [,39] [,40] [,41] [,42] #> [1,] "2.2.2_0.0" "2.2.4_0.0" "2.4.2_0.0" "4.2.2_0.0" "2.2.2_0.0" "2.2.1_0.0" #> [2,] "3.1.1_0.0" "1.1.1_0.0" "1.1.2_0.0" "1.2.2_0.0" "2.2.4_0.0" "2.4.4_0.0" #> [3,] "1.2.2_0.0" "2.2.1_0.0" "2.1.4_0.0" "1.4.4_0.0" "4.4.1_0.0" "4.1.4_0.0" #> [4,] "2.1.1_0.0" "1.1.1_0.0" "1.1.4_0.0" "1.4.3_0.0" "4.3.1_0.0" "3.1.1_0.0" #> [5,] "3.4.4_0.0" "4.4.2_0.0" "4.2.2_0.0" "2.2.4_0.0" "2.4.3_0.0" "4.3.4_0.0" #> [6,] "1.4.2_0.0" "4.2.2_0.0" "2.2.4_0.0" "2.4.3_0.0" "4.3.2_0.0" "3.2.2_0.0" #> [7,] "1.1.3_0.0" "1.3.3_0.0" "3.3.3_0.0" "3.3.2_0.0" "3.2.2_0.0" "2.2.3_0.0" #> [8,] "4.2.3_0.0" "2.3.3_0.0" "3.3.1_0.0" "3.1.1_0.0" "1.1.1_0.0" "1.1.4_0.0" #> [9,] "4.2.3_0.0" "2.3.4_0.0" "3.4.4_0.0" "4.4.4_0.0" "4.4.2_0.0" "4.2.3_0.0" #> [10,] "1.2.2_0.0" "2.2.4_0.0" "2.4.1_0.0" "4.1.1_0.0" "1.1.1_0.0" "1.1.2_0.0" #> [11,] "4.2.1_0.0" "2.1.1_0.0" "1.1.2_0.0" "1.2.2_0.0" "2.2.4_0.0" "2.4.2_0.0" #> [12,] "3.1.2_0.0" "1.2.2_0.0" "2.2.4_0.0" "2.4.2_0.0" "4.2.3_0.0" "2.3.2_0.0" #> [,43] [,44] [,45] [,46] [,47] [,48] #> [1,] "2.1.2_0.0" "1.2.3_0.0" "2.3.3_0.0" "3.3.2_0.0" "3.2.1_0.0" "2.1.4_0.0" #> [2,] "4.4.2_0.0" "4.2.1_0.0" "2.1.4_0.0" "1.4.1_0.0" "4.1.4_0.0" "1.4.1_0.0" #> [3,] "1.4.4_0.0" "4.4.4_0.0" "4.4.2_0.0" "4.2.2_0.0" "2.2.1_0.0" "2.1.2_0.0" #> [4,] "1.1.3_0.0" "1.3.2_0.0" "3.2.1_0.0" "2.1.1_0.0" "1.1.3_0.0" "1.3.1_0.0" #> [5,] "3.4.2_0.0" "4.2.2_0.0" "2.2.2_0.0" "2.2.1_0.0" "2.1.3_0.0" "1.3.2_0.0" #> [6,] "2.2.4_0.0" "2.4.4_0.0" "4.4.2_0.0" "4.2.3_0.0" "2.3.3_0.0" "3.3.3_0.0" #> [7,] "2.3.1_0.0" "3.1.3_0.0" "1.3.4_0.0" "3.4.1_0.0" "4.1.2_0.0" "1.2.1_0.0" #> [8,] "1.4.1_0.0" "4.1.2_0.0" "1.2.1_0.0" "2.1.2_0.0" "1.2.1_0.0" "2.1.1_0.0" #> [9,] "2.3.1_0.0" "3.1.3_0.0" "1.3.2_0.0" "3.2.3_0.0" "2.3.4_0.0" "3.4.2_0.0" #> [10,] "1.2.4_0.0" "2.4.4_0.0" "4.4.2_0.0" "4.2.3_0.0" "2.3.1_0.0" "3.1.4_0.0" #> [11,] "4.2.4_0.0" "2.4.3_0.0" "4.3.1_0.0" "3.1.2_0.0" "1.2.3_0.0" "2.3.2_0.0" #> [12,] "3.2.2_0.0" "2.2.4_0.0" "2.4.3_0.0" "4.3.4_0.0" "3.4.4_0.0" "4.4.3_0.0"