correct_counts {sctransform}

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

Description

This version does not need a matrix of Pearson residuals. It takes the count matrix as input and calculates the residuals on the fly. The corrected UMI counts will be rounded to the nearest integer and negative values clipped to 0.

Usage

correct_counts(
  x,
  umi,
  cell_attr = x$cell_attr,
  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

umi

The count matrix

cell_attr

Provide cell meta data holding latent data info

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_counts(vst_out, pbmc)