sctransform (version 0.4.3)

get_model_var: Return average variance under negative binomial model

Description

This is based on the formula var = mu + mu^2 / theta

Usage

get_model_var(
  vst_out,
  cell_attr = vst_out$cell_attr,
  use_nonreg = FALSE,
  bin_size = 256,
  verbosity = 2
)

Value

A named vector of variances (the average across all cells), one entry per gene.

Arguments

vst_out

The output of a vst run

cell_attr

Data frame of cell meta data

use_nonreg

Use the non-regularized parameter estimates; boolean; default is FALSE

bin_size

Number of genes to put in each bin (to show progress)

verbosity

An integer specifying the verbosity level: 0 (silent, no messages), 1 (show messages only), or 2 (show messages and progress bars); default is 2

Examples

# \donttest{
vst_out <- vst(pbmc, return_cell_attr = TRUE)
res_var <- get_model_var(vst_out)
# }