create_simulation_data: function generates set of RDS files containing n-gram...

In jakubkala/QuiPTsim:

Description

function generates set of RDS files containing n-gram matrices

Usage

create_simulation_data(
  replications,
  seq_nums,
  seq_lengths,
  num_motifs,
  alphabet,
  path,
  title,
  save_files = FALSE,
  motifProbs = NULL,
  seqProbs = NULL,
  fraction = 0.5,
  n = 4,
  d = 6
)

Arguments

replications	number of matrices' generation for each set of parameters
seq_nums	vector of sequences' numbers
seq_lengths	vector of sequences' lengths
num_motifs	vector of number of motifs to be injected
alphabet	elements used to build both sequence and motif
path	file path of RDS files
title	simulation name
save_files	triggers if RDS will be saved
motifProbs	alphabet probabilites for motifs
seqProbs	alphabet probabilites for sequences
fraction	fraction of positive sequences
n	maximum number of alphabet elements in motif
d	maximum number of gaps in motif

Value

data frame with RDS files' details

Examples

alph <- letters[1:4]
reps <- 10
n_seq <- c(10)
l_seq <- c(10)
n_motifs <- c(1, 2)
path = "./"
results <- create_simulation_data(reps, n_seq, l_seq, n_motifs, alph, path, "SEQ",FALSE)

alph <- letters[1:4]
reps <- 3
n_seq <- c(10)
l_seq <- c(10)
n_motifs <- 1
results <- create_simulation_data(reps, n_seq, l_seq, n_motifs, alph,
                                 path, "SEQ", FALSE,
                                 motifProbs = c(0.7, 0.1, 0.1, 0.1),
                                 seqProbs = c(0.7, 0.1, 0.1, 0.1),
                                 n = 4, d = 4)

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