create_trainer: Create a YamatClassifierTrainer object.

In markgene/yamatClassifier: Yet Another Methylation Array Toolkit: Classifier

Create a YamatClassifierTrainer object.

Description

Create a YamatClassifierTrainer object.

Usage

create_trainer(
  idat_dir,
  targets,
  output,
  probes = NULL,
  beta_offset = 100,
  probes_rda = "probes.Rda",
  preprocessed_dir = "dkfz_preprocessed",
  batch_effect_explore_dir = "batch_effect_explore",
  meth_rda = "meth.Rda",
  unmeth_rda = "unmeth.Rda",
  beta_value_rda = "beta_value.Rda",
  beta_value_adjusted_rda = "beta_value_adjusted.Rda",
  trainer_rda = "trainer.Rda",
  overwrite = FALSE
)

Arguments

idat_dir	IDAT file directory.
targets	data.frame of targets. See read.metharray.exp.
output	output directory.
probes	a character vector of probes.
beta_offset	offset to calculate beta ratio.
probes_rda	probes Rda file.
preprocessed_dir	preprocessed file directory.
batch_effect_explore_dir	batch effect exploratory analysis directory.
meth_rda	meth Rda file.
unmeth_rda	unmeth Rda file.
beta_value_rda	beta value Rda file.
beta_value_adjusted_rda	adjusted beta value Rda file.
trainer_rda	YamatClassifierTrainer object Rda file.
overwrite	A bool if overwrite the result files.

Value

A S3 object of YamatClassifierTrainer class.

markgene/yamatClassifier documentation built on Oct. 14, 2024, 2:36 a.m.