generate_sequences: function counts n-grams in given sequences

In jakubkala/QuiPTsim:

Description

function counts n-grams in given sequences

Usage

generate_sequences(
  n_seq,
  l_seq,
  alphabet,
  motifs_list,
  n_motifs,
  fraction = 0.5,
  seqProbs = NULL,
  n = 4,
  d = 6
)

Arguments

n_seq	number of sequences to be generated
l_seq	sequence length
alphabet	elements used to build sequence
motifs_list	list of injected motifs
n_motifs	number of motifs injected to each positive sequence
fraction	TODO: add fraction: of positive sequences / change approach
seqProbs	alphabet probabilites 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
len <- 1200
alph <- letters[1:4]
motifs <- generate_motifs(alph, 2)
results <- generate_sequences(n_seq, len, alph, motifs, 1)
results <- generate_sequences(n_seq, len, alph, motifs, 1, seqProbs = c(0.7, 0.1, 0.1, 0.1))
results
attributes(results)

jakubkala/QuiPTsim documentation built on Jan. 17, 2022, 11:27 p.m.