run_alignment_by_2D

Source: R/run_alignment_by_2D.R

Correct batch effects.

run_alignment_by_2D(
  object,
  quantile = 0.95,
  K = 30,
  selected = NULL,
  Nclust = NULL,
  steps = 20,
  gra_steps = 10,
  NCell = 100
)

Arguments

object

A dmatch class object.
quantile

The minimum number of the data points regarded as good points.
K

The number of PCs for correcting batch effects, default is 30.
selected

The clusters which are used as anchors to study batch effects.
NCell

The smallest number of cells that a selected cluster (as anchors) should have. Default is 100, and recommend no less than 5 percent of the sample size.

Value

A dmatch class object which has slots storing raw.data, batch.id, PCA, and more information. Specfically, run_alignment_by_2D.results slot stores information for the reference sample, the original and corrected version of the other sample, and the celltype labels for both samples.