explore_batch_effect_unmeth_pca_compute: Perform PCA on unmeth

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

Perform PCA on unmeth

Description

Perform PCA on unmeth

Usage

explore_batch_effect_unmeth_pca_compute(
  trainer,
  batch_name,
  top_n = 20000,
  k = 50,
  seed = 1,
  threshold = 0.9,
  unmeth_pca_rda = "unmeth_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 unmethod of determining PC number. In brief, the unmethod 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.
unmeth_pca_rda	Rda file for unmeth PCA result.

Value

a ggplot object.

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