count_ngrams: Count n-grams in sequences

Description Usage Arguments Details Value Note See Also Examples

View source: R/count_ngrams.R

Description

Counts all n-grams or position-specific n-grams present in the input sequence(s).

Usage

1
count_ngrams(seq, n, u, d = 0, pos = FALSE, scale = FALSE, threshold = 0)

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.

scale

logical, if TRUE output data is normalized. May be applied only to the counts of n-grams without position information. See Details.

threshold

integer, if not equal to 0, data is binarized into two groups (larger or equal to threshold vs. smaller than threshold).

Details

A distance vector should be always n - 1 in length. For example when n = 3, d = c(1,2) means A_A__A. For n = 4, d = c(2,0,1) means A__AA_A. If vector d has length 1, it is recycled to length n - 1.

n-gram names follow a specific convention and have three parts for position-specific n-grams and two parts otherwise. The parts are separated by _. The . symbol is used to separate elements within a part. The general naming scheme is POSITION_NGRAM_DISTANCE. The optional POSITION part of the name indicates the actual position of the n-gram in the sequence(s) and will be present only if pos = TRUE. This part is always a single integer. The NGRAM part of the name is a sequence of elements in the n-gram. For example, 4.2.2 indicates the n-gram 422 (e.g. TCC). The DISTANCE part of the name is a vector of distance(s). For example, 0.0 indicates zero distances (continuous n-grams), while 1.2 represents distances for the n-gram A_A__A.

Examples of n-gram names:

Value

a simple_triplet_matrix where columns represent n-grams and rows sequences. See Details for specifics of the naming convention.

Note

By default, the counted n-gram data is stored in a memory-saving format. To convert an object to a 'classical' matrix use the as.matrix function. See examples for further information.

See Also

Create vector of possible n-grams: create_ngrams.

Extract n-grams from sequence(s): seq2ngrams.

Get indices of n-grams: get_ngrams_ind.

Count n-grams for multiple values of n: count_multigrams.

Count only specified n-grams: count_specified.

Examples

1
2
3
4
5
6
7
# count trigrams without position information for nucleotides
count_ngrams(sample(1L:4, 50, replace = TRUE), 3, 1L:4, pos = FALSE)
# count position-specific trigrams from multiple nucleotide sequences
seqs <- matrix(sample(1L:4, 600, replace = TRUE), ncol = 50)
ngrams <- count_ngrams(seqs, 3, 1L:4, pos = TRUE)
# output results of the n-gram counting to screen
as.matrix(ngrams)

Example output

Loading required package: slam
A 1x64 simple triplet matrix.
      1_1.1.1_0.0 2_1.1.1_0.0 3_1.1.1_0.0 4_1.1.1_0.0 5_1.1.1_0.0 6_1.1.1_0.0
 [1,]           0           0           0           0           0           0
 [2,]           0           0           0           0           0           0
 [3,]           0           0           0           0           0           0
 [4,]           0           0           0           0           0           0
 [5,]           0           0           0           0           0           0
 [6,]           0           0           0           0           0           0
 [7,]           0           0           0           0           0           0
 [8,]           0           0           0           0           0           0
 [9,]           0           0           0           0           0           0
[10,]           0           0           0           0           0           0
[11,]           0           0           0           0           0           0
[12,]           0           0           0           0           0           0
      7_1.1.1_0.0 8_1.1.1_0.0 9_1.1.1_0.0 10_1.1.1_0.0 11_1.1.1_0.0
 [1,]           0           0           0            0            0
 [2,]           0           0           1            0            0
 [3,]           0           0           0            0            0
 [4,]           0           0           0            0            0
 [5,]           0           0           0            0            0
 [6,]           0           0           0            0            0
 [7,]           0           0           0            0            0
 [8,]           0           0           0            0            0
 [9,]           0           0           0            0            0
[10,]           0           0           0            0            0
[11,]           0           0           0            0            0
[12,]           0           0           0            0            0
      12_1.1.1_0.0 13_1.1.1_0.0 14_1.1.1_0.0 15_1.1.1_0.0 16_1.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            1
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            1            0            0
[12,]            0            0            0            0            0
      17_1.1.1_0.0 18_1.1.1_0.0 19_1.1.1_0.0 20_1.1.1_0.0 21_1.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            1            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            1            0            0            0
      22_1.1.1_0.0 23_1.1.1_0.0 24_1.1.1_0.0 25_1.1.1_0.0 26_1.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      27_1.1.1_0.0 28_1.1.1_0.0 29_1.1.1_0.0 30_1.1.1_0.0 31_1.1.1_0.0
 [1,]            1            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            1
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      32_1.1.1_0.0 33_1.1.1_0.0 34_1.1.1_0.0 35_1.1.1_0.0 36_1.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            1
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      37_1.1.1_0.0 38_1.1.1_0.0 39_1.1.1_0.0 40_1.1.1_0.0 41_1.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            1            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            1            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      42_1.1.1_0.0 43_1.1.1_0.0 44_1.1.1_0.0 45_1.1.1_0.0 46_1.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      47_1.1.1_0.0 48_1.1.1_0.0 1_2.1.1_0.0 2_2.1.1_0.0 3_2.1.1_0.0 4_2.1.1_0.0
 [1,]            0            0           0           0           0           0
 [2,]            0            0           0           0           0           0
 [3,]            0            0           0           0           0           0
 [4,]            0            0           0           0           0           0
 [5,]            0            0           0           0           0           0
 [6,]            0            0           0           0           0           0
 [7,]            0            0           0           0           0           0
 [8,]            0            0           0           0           0           0
 [9,]            0            0           0           0           0           0
[10,]            0            0           0           0           0           0
[11,]            0            0           0           0           0           0
[12,]            0            0           0           0           0           0
      5_2.1.1_0.0 6_2.1.1_0.0 7_2.1.1_0.0 8_2.1.1_0.0 9_2.1.1_0.0 10_2.1.1_0.0
 [1,]           0           0           0           0           0            0
 [2,]           0           0           0           0           0            0
 [3,]           0           1           0           0           0            0
 [4,]           0           0           0           0           0            0
 [5,]           0           0           0           0           0            0
 [6,]           0           0           0           0           0            0
 [7,]           0           0           0           0           0            0
 [8,]           0           0           0           0           0            0
 [9,]           0           0           0           0           0            0
[10,]           0           0           0           0           0            0
[11,]           0           0           0           0           0            0
[12,]           0           0           1           0           0            0
      11_2.1.1_0.0 12_2.1.1_0.0 13_2.1.1_0.0 14_2.1.1_0.0 15_2.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      16_2.1.1_0.0 17_2.1.1_0.0 18_2.1.1_0.0 19_2.1.1_0.0 20_2.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            1            0            0            0
      21_2.1.1_0.0 22_2.1.1_0.0 23_2.1.1_0.0 24_2.1.1_0.0 25_2.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      26_2.1.1_0.0 27_2.1.1_0.0 28_2.1.1_0.0 29_2.1.1_0.0 30_2.1.1_0.0
 [1,]            1            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            1            0
 [6,]            0            0            0            0            0
 [7,]            0            0            1            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            1
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      31_2.1.1_0.0 32_2.1.1_0.0 33_2.1.1_0.0 34_2.1.1_0.0 35_2.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            1            0            0            0
      36_2.1.1_0.0 37_2.1.1_0.0 38_2.1.1_0.0 39_2.1.1_0.0 40_2.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            1            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            1            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            1            0            0            0
[12,]            0            0            0            0            0
      41_2.1.1_0.0 42_2.1.1_0.0 43_2.1.1_0.0 44_2.1.1_0.0 45_2.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            1            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      46_2.1.1_0.0 47_2.1.1_0.0 48_2.1.1_0.0 1_3.1.1_0.0 2_3.1.1_0.0
 [1,]            0            0            0           0           0
 [2,]            0            0            0           0           0
 [3,]            0            0            0           0           0
 [4,]            0            0            0           0           0
 [5,]            0            0            0           0           0
 [6,]            0            0            0           0           0
 [7,]            0            0            0           0           0
 [8,]            0            0            0           0           0
 [9,]            0            0            0           0           0
[10,]            0            0            0           0           0
[11,]            0            0            0           0           0
[12,]            0            0            0           0           0
      3_3.1.1_0.0 4_3.1.1_0.0 5_3.1.1_0.0 6_3.1.1_0.0 7_3.1.1_0.0 8_3.1.1_0.0
 [1,]           0           0           0           0           0           0
 [2,]           0           0           0           0           0           0
 [3,]           0           0           0           0           0           0
 [4,]           0           0           0           0           0           0
 [5,]           0           0           0           0           0           0
 [6,]           0           0           0           0           0           0
 [7,]           0           0           0           0           0           0
 [8,]           0           0           0           0           0           0
 [9,]           0           0           0           0           0           0
[10,]           0           0           0           0           0           0
[11,]           0           0           0           0           0           0
[12,]           0           0           0           0           0           0
      9_3.1.1_0.0 10_3.1.1_0.0 11_3.1.1_0.0 12_3.1.1_0.0 13_3.1.1_0.0
 [1,]           0            0            0            0            0
 [2,]           0            0            0            0            0
 [3,]           0            0            0            0            0
 [4,]           0            0            0            0            0
 [5,]           0            0            0            0            0
 [6,]           0            0            0            0            0
 [7,]           0            0            0            0            0
 [8,]           0            0            0            0            0
 [9,]           0            0            0            0            0
[10,]           0            0            0            0            0
[11,]           0            0            0            0            1
[12,]           0            0            0            0            0
      14_3.1.1_0.0 15_3.1.1_0.0 16_3.1.1_0.0 17_3.1.1_0.0 18_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            1            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      19_3.1.1_0.0 20_3.1.1_0.0 21_3.1.1_0.0 22_3.1.1_0.0 23_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            1            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      24_3.1.1_0.0 25_3.1.1_0.0 26_3.1.1_0.0 27_3.1.1_0.0 28_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            1            0            0
[12,]            0            0            0            0            0
      29_3.1.1_0.0 30_3.1.1_0.0 31_3.1.1_0.0 32_3.1.1_0.0 33_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            1            0            0            0            0
[12,]            0            0            0            0            0
      34_3.1.1_0.0 35_3.1.1_0.0 36_3.1.1_0.0 37_3.1.1_0.0 38_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            1            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      39_3.1.1_0.0 40_3.1.1_0.0 41_3.1.1_0.0 42_3.1.1_0.0 43_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      44_3.1.1_0.0 45_3.1.1_0.0 46_3.1.1_0.0 47_3.1.1_0.0 48_3.1.1_0.0
 [1,]            0            0            0            0            0
 [2,]            0            0            0            0            0
 [3,]            0            0            0            0            0
 [4,]            0            0            0            0            0
 [5,]            0            0            0            0            0
 [6,]            0            0            0            0            0
 [7,]            0            0            0            0            0
 [8,]            0            0            0            0            0
 [9,]            0            0            0            0            0
[10,]            0            0            0            0            0
[11,]            0            0            0            0            0
[12,]            0            0            0            0            0
      1_4.1.1_0.0 2_4.1.1_0.0 3_4.1.1_0.0 4_4.1.1_0.0 5_4.1.1_0.0 6_4.1.1_0.0
 [1,]           0           0           0           0           0           0
 [2,]           0           0           0           0           0           0
 [3,]           0           0           0           0           0           0
 [4,]           0           0           0           0           0           0
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