GetOptimalPcs: Perform PCA with the optimal number of principal components.

In kharchenkolab/dropestr: Preprocessing of Droplet-Based Single-Cell RNA-Seq Data

Description

Perform PCA with the optimal number of principal components.

Usage

GetOptimalPcs(
  data,
  explained.var.required = 0.98,
  max.pcs = 3,
  loadings.filt.threshold = 0.075
)

Arguments

data	data for low-quality cells filtration
explained.var.required	numeric Minimal fraction of explained variance (default=0.98)
max.pcs	numeric Maximal number of output principal components (default=3)
loadings.filt.threshold	numeric Minimal contribution to loadings, with which feature is considered as used (default=7.5e-2)

Value

List with the PCA results:

total.variance.explained	fraction of the explained variance.
pca.data	transformed data with the optimal number of principal components.
used.features	features, which contribute to pca.data.

kharchenkolab/dropestr documentation built on Sept. 18, 2020, 2:14 a.m.