Generate a kmer Matrix

This function calculates the frequency of each kmer for each DNA sequence.

Usage

kmer_matrix(
  sequences,
  kmer_length,
  max_gap = 0,
  mask = NULL,
  add_mask = FALSE,
  from_range = 1,
  to_range = NULL,
  set_rownames = FALSE
)

Arguments

sequences

A vector of strings with DNA sequences ('T', 'C', 'G', 'A' or 'N').

kmer_length

The length of the kmers to be considered.

max_gap

The maximum length of a gap to be considered in the pattern. Default: 0

mask

a string the length of kmer_length where 'N' indicates a wildcard position (default NULL - no mask).

add_mask

if TRUE, the result of the mask will be added to the non-masked kmers. Otherwise - only the masked kmers would be returned.

from_range

Sequences will be considered only from position from_range.

to_range

Sequences will be considered only up to position to_range (default NULL - using the length of the sequences).

set_rownames

If TRUE, the rownames of the matrix will be set to the sequences (default FALSE).

Value

A matrix where rows are the number of sequences, columns are the kmers and the values are the number of occurrences of each kmer.

Examples

kmer_matrix(c("ATCG", "TCGA", "ATAT"), 2)
#>      CG AT TC GA TA
#> [1,]  1  1  1  0  0
#> [2,]  1  0  1  1  0
#> [3,]  0  2  0  0  1
kmer_matrix(c("ATCG", "TCGA", "ATAT"), 3)
#>      TCG ATC CGA TAT ATA
#> [1,]   1   1   0   0   0
#> [2,]   1   0   1   0   0
#> [3,]   0   0   0   1   1
kmer_matrix(c("ATCG", "TCGA", "ATAT"), 3, mask = "ATN")
#>      TCN ATN CGN TAN
#> [1,]   1   1   0   0
#> [2,]   1   0   1   0
#> [3,]   0   1   0   1