sctransform: correct_counts – R documentation

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correct_counts

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,
  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
`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)

sctransform

Variance Stabilizing Transformations for Single Cell UMI Data

v0.3.2

GPL-3 | file LICENSE

Authors

Christoph Hafemeister [aut, cre] (<https://orcid.org/0000-0001-6365-8254>)

Initial release