sctransform (version 0.2.1)

correct: Correct data by setting all latent factors to their median values and reversing the regression model

Description

Correct data by setting all latent factors to their median values and reversing the regression model

Usage

correct(x, data = "y", cell_attr = x$cell_attr, do_round = TRUE,
  do_pos = TRUE, show_progress = TRUE)

Arguments

x

A list that provides model parameters and optionally meta data; use output of vst function

data

The name of the entry in x that holds the data

cell_attr

Provide cell meta data holding latent data info

do_round

Round the result to integers

do_pos

Set negative values in the result to zero

show_progress

Whether to print progress bar

Value

Corrected data as UMI counts

Examples

# NOT RUN {
vst_out <- vst(pbmc, return_cell_attr = TRUE)
umi_corrected <- correct(vst_out)
# }
# NOT RUN {
# }