explore_batch_effect_beta_value_pca_compute: Perform PCA on beta_value

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

Perform PCA on beta_value

Description

Perform PCA on beta_value

Usage

explore_batch_effect_beta_value_pca_compute(
  trainer,
  batch_name,
  top_n = 20000,
  k = 50,
  seed = 1,
  threshold = 0.9,
  beta_value_pca_rda = "beta_value_pca.Rda"
)

Arguments

trainer	A S3 object of YamatClassifierTrainer class.
batch_name	column name of batch in the targets attribute of YamatClassifierTrainer object.
top_n	an integer of the most variable N loci for relative log expression (RLE) analysis.
k	Number of eigenvalues requested.
seed	A numeric number of seed used for Capper's beta_valueod of determining PC number. In brief, the beta_valueod shuffles features across samples and determine the PC number by comparing the maximum of eigen values from the randomization.
threshold	A numeric scalar between 0 to 1 of the threshold of the fraction of variance to choose PC number. Default to 0.9.
beta_value_pca_rda	Rda file for beta_value PCA result.

Value

a ggplot object.

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