SuperCell (version 1.0)

supercell_prcomp: compute PCA for super-cell data (sample-weighted data)

Description

compute PCA for super-cell data (sample-weighted data)

Usage

supercell_prcomp(
  X,
  genes.use = NULL,
  genes.exclude = NULL,
  supercell_size = NULL,
  k = 20,
  do.scale = TRUE,
  do.center = TRUE,
  fast.pca = TRUE,
  seed = 12345
)

Value

the same object as prcomp result

Arguments

X

super-cell transposed gene expression matrix (! where rows represent super-cells and cols represent genes)

genes.use

genes to use for dimensionality reduction

genes.exclude

genes to exclude from dimensionaloty reduction

supercell_size

a vector with supercell sizes (ordered the same way as in X)

k

number of components to compute

do.scale

scale data before PCA

do.center

center data before PCA

fast.pca

whether to run fast PCA (works for datasets with |super-cells| > 50)

seed

a seed to use for set.seed