get_start_ind: Computes start position of samples

In GenomeNet/deepG: Deep Learning for Genome Sequence Data

Computes start position of samples

Description

Helper function for data generators. Computes start positions in sequence where samples can be extracted, given maxlen, step size and ambiguous nucleotide constraints.

Usage

get_start_ind(
  seq_vector,
  length_vector,
  maxlen,
  step,
  train_mode = "label",
  discard_amb_nuc = FALSE,
  vocabulary = c("A", "C", "G", "T")
)

Arguments

seq_vector	Vector of character sequences.
length_vector	Length of sequences in seq_vector.
maxlen	Length of one predictor sequence.
step	Distance between samples from one entry in seq_vector.
train_mode	Either "lm" for language model or "label" for label classification.
discard_amb_nuc	Whether to discard all samples that contain characters outside vocabulary.
vocabulary	Vector of allowed characters. Characters outside vocabulary get encoded as specified in ambiguous_nuc.

Value

A numeric vector.

Examples

seq_vector <- c("AAACCCNNNGGGTTT")
get_start_ind(
  seq_vector = seq_vector,
  length_vector = nchar(seq_vector),
  maxlen = 4,
  step = 2,
  train_mode = "label",
  discard_amb_nuc = TRUE,
  vocabulary = c("A", "C", "G", "T"))
  

GenomeNet/deepG documentation built on Dec. 24, 2024, 12:11 p.m.