calc_pca: Calculate principal components using irlba

In hesselberthlab/scrunchy: Single Cell Reconstruction of Functional Heterogeneity

Description

Calculate principal components using irlba

Usage

calc_pca(fsce, expt = "rnaseq", genes = NULL, n_pcs = 20,
  scale = TRUE, seed = NULL)

Arguments

fsce	FunctionalSingleCellExperiment object
expt	Data to use for calculating variable features (default is rnaseq). Must be present in names(fsce).
genes	vector of genes to include in PCA (default is all genes)
n_pcs	number of principle components to return
scale	If TRUE, perform PCA on input on scaled data
seed	seed for reproducible result

Value

fsce with PCA values added to reducedDims

hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.