correct {sctransform}

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,
  as_is = FALSE,
  do_round = TRUE,
  do_pos = TRUE,
  scale_factor = NA,
  verbosity = 2,
  verbose = NULL,
  show_progress = NULL
)

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

as_is

Use cell attributes as is and do not use the median; set to TRUE if you want to manually control the values of the latent factors; default is FALSE

do_round

Round the result to integers

do_pos

Set negative values in the result to zero

scale_factor

Replace all values of UMI in the regression model by this value. Default is NA which uses median of total UMI as the latent factor.

verbosity

An integer specifying whether to show only messages (1), messages and progress bars (2) or nothing (0) while the function is running; default is 2

verbose

Deprecated; use verbosity instead

show_progress

Deprecated; use verbosity instead

Value

Corrected data as UMI counts

Examples

vst_out <- vst(pbmc, return_cell_attr = TRUE)
umi_corrected <- correct(vst_out)