sctransform (version 0.2.1)

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, show_progress = TRUE)

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)

show_progress

Whether to print progress bar

Value

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

Examples

# NOT RUN {
vst_out <- vst(pbmc)
res_var <- get_model_var(vst_out)
# }
# NOT RUN {
# }