initializeGenerators: Initializes generators defined by labelByFolderGenerator...

Usage Arguments

View source: R/generators.R

Usage

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initializeGenerators(
  directories,
  format = "fasta",
  batch.size = 256,
  maxlen = 250,
  max_iter = 10000,
  vocabulary = c("a", "c", "g", "t"),
  verbose = FALSE,
  randomFiles = FALSE,
  step = 1,
  showWarnings = FALSE,
  seed = 1234,
  shuffleFastaEntries = FALSE,
  numberOfFiles = NULL,
  fileLog = NULL,
  reverseComplements = FALSE,
  val = FALSE
)

Arguments

directories

Vector of paths to folder containing fasta files. Files in one folder should belong to one class.

format

File format.

batch.size

Number of batches, will get rounded to be multiple of number of targets if necessary.

maxlen

Length of predictor sequence.

max_iter

Stop after max_iter number of iterations failed to produce a new batch.

vocabulary

Vector of allowed characters, character outside vocabulary get encoded as 0-vector.

verbose

Whether to show message.

randomFiles

Logical, whether to go through files randomly or sequential.

step

How often to take a sample.

showWarnings

Logical, give warning if character outside vocabulary appears.

seed

Sets seed for set.seed function, for reproducible results when using randomFiles or shuffleFastaEntries

shuffleFastaEntries

Logical, shuffle fasta entries.

numberOfFiles

Use only specified number of files, ignored if greater than number of files in directories.

fileLog

Write name of files to csv file if path is specified.

reverseComplements

Logical, half of batch contains sequences and other its reverse complements. Reverse complement is given by reversed order of sequence and switching A/T and C/G. batch.size argument has to be even, otherwise 1 will be added to batch.size

val

Logical, call initialized generarator "genY" or "genValY" where Y is an integer between 1 and length of directories.


hiddengenome/deepG documentation built on April 16, 2020, 1:38 a.m.