explore_batch_effect_meth_pca_compute: Perform PCA on meth

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

Perform PCA on meth

Description

Perform PCA on meth

Usage

explore_batch_effect_meth_pca_compute(
  trainer,
  batch_name,
  top_n = 20000,
  k = 50,
  seed = 1,
  threshold = 0.9,
  meth_pca_rda = "meth_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 method of determining PC number. In brief, the method 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.
meth_pca_rda	Rda file for meth PCA result.

Value

a ggplot object.

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