count_ngrams: Count n-grams in sequences
In biogram: N-Gram Analysis of Biological Sequences
Description
Usage
Arguments
Details
Value
Note
See Also
Examples
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:
46_4.4.4_0.1 : trigram 44_4 on position 46
12_2.1_2 : bigram 2__1 on position 12
8_1.1.1_0.0 : continuous trigram 111 on position 8
1.1.1_0.0 : continuous trigram 111 without position information
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
[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 1 0 0
[11,] 0 0 0 0 0 0
[12,] 0 0 0 0 0 0
7_4.1.1_0.0 8_4.1.1_0.0 9_4.1.1_0.0 10_4.1.1_0.0 11_4.1.1_0.0
[1,] 0 0 0 0 0
[2,] 0 1 0 0 0
[3,] 0 0 0 1 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 1 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
12_4.1.1_0.0 13_4.1.1_0.0 14_4.1.1_0.0 15_4.1.1_0.0 16_4.1.1_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 0 0
[8,] 0 0 1 0 0
[9,] 0 0 0 0 0
[10,] 0 0 0 0 1
[11,] 0 0 0 0 0
[12,] 0 0 1 0 0
17_4.1.1_0.0 18_4.1.1_0.0 19_4.1.1_0.0 20_4.1.1_0.0 21_4.1.1_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 1 0 0
[8,] 0 1 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
22_4.1.1_0.0 23_4.1.1_0.0 24_4.1.1_0.0 25_4.1.1_0.0 26_4.1.1_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 1
27_4.1.1_0.0 28_4.1.1_0.0 29_4.1.1_0.0 30_4.1.1_0.0 31_4.1.1_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
32_4.1.1_0.0 33_4.1.1_0.0 34_4.1.1_0.0 35_4.1.1_0.0 36_4.1.1_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
37_4.1.1_0.0 38_4.1.1_0.0 39_4.1.1_0.0 40_4.1.1_0.0 41_4.1.1_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,] 1 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
42_4.1.1_0.0 43_4.1.1_0.0 44_4.1.1_0.0 45_4.1.1_0.0 46_4.1.1_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_4.1.1_0.0 48_4.1.1_0.0 1_1.2.1_0.0 2_1.2.1_0.0 3_1.2.1_0.0 4_1.2.1_0.0
[1,] 0 0 0 0 0 0
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[3,] 1 1 1 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 1 0 0 0 0
[8,] 0 0 0 0 0 1
[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_4.4.4_0.0 8_4.4.4_0.0 9_4.4.4_0.0 10_4.4.4_0.0 11_4.4.4_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 0
[11,] 0 0 0 0 0
[12,] 0 0 0 0 0
12_4.4.4_0.0 13_4.4.4_0.0 14_4.4.4_0.0 15_4.4.4_0.0 16_4.4.4_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
17_4.4.4_0.0 18_4.4.4_0.0 19_4.4.4_0.0 20_4.4.4_0.0 21_4.4.4_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
22_4.4.4_0.0 23_4.4.4_0.0 24_4.4.4_0.0 25_4.4.4_0.0 26_4.4.4_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_4.4.4_0.0 28_4.4.4_0.0 29_4.4.4_0.0 30_4.4.4_0.0 31_4.4.4_0.0
[1,] 0 0 0 1 0
[2,] 0 0 0 0 0
[3,] 0 0 0 0 0
[4,] 0 0 0 1 1
[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
32_4.4.4_0.0 33_4.4.4_0.0 34_4.4.4_0.0 35_4.4.4_0.0 36_4.4.4_0.0
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
[3,] 0 0 0 0 0
[4,] 1 0 0 0 0
[5,] 1 0 0 0 0
[6,] 0 0 0 0 0
[7,] 0 0 0 0 1
[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
37_4.4.4_0.0 38_4.4.4_0.0 39_4.4.4_0.0 40_4.4.4_0.0 41_4.4.4_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
42_4.4.4_0.0 43_4.4.4_0.0 44_4.4.4_0.0 45_4.4.4_0.0 46_4.4.4_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 1
[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_4.4.4_0.0 48_4.4.4_0.0
[1,] 0 0
[2,] 0 0
[3,] 0 0
[4,] 0 0
[5,] 0 0
[6,] 0 0
[7,] 0 0
[8,] 0 0
[9,] 0 0
[10,] 0 0
[11,] 0 0
[12,] 0 0
biogram documentation built on March 31, 2020, 5:14 p.m.
R Package Documentation
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Description Usage Arguments Details Value Note See Also Examples
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 |
|
u |
|
d |
|
pos |
|
scale |
|
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:
46_4.4.4_0.1 : trigram 44_4 on position 46
12_2.1_2 : bigram 2__1 on position 12
8_1.1.1_0.0 : continuous trigram 111 on position 8
1.1.1_0.0 : continuous trigram 111 without position information
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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