correct: Correct data by setting all latent factors to their median...

In ChristophH/sctransform: Variance Stabilizing Transformations for Single Cell UMI Data

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)

ChristophH/sctransform documentation built on Oct. 22, 2023, 3:28 p.m.