K-mer data generation — generate_kmer

This function generates sequences with provided motifs and constructs k-mer representation table based on this data.

generate_kmer_data(
  n_seq,
  sequence_length,
  alphabet,
  motifs,
  n_injections,
  fraction = 0.5,
  seqProbs = NULL,
  n = 4,
  d = 6
)

Arguments

n_seq: number of sequences to be generated
sequence_length: sequence length
alphabet: elements used to build sequence
motifs: list of motifs
n_injections: maximal number of motifs injected to each positive sequence (from 1 to n_injections will be injected)
fraction: fraction of positive sequences
seqProbs: alphabet probabilities for sequences
n: maximum number of alphabet elements in n-gram
d: maximum number of gaps in n-gram

Value

generated sequences

Examples

n_seq <- 20
sequence_length <- 20
alph <- letters[1:4]
motifs <- generate_motifs(alph, 3, 3, 4, 6)
results <- generate_kmer_data(n_seq, sequence_length, alph, motifs, 1)