Correct data by setting all latent factors to their median values and reversing the regression model
Correct data by setting all latent factors to their median values and reversing the regression model
correct( x, data = "y", cell_attr = x$cell_attr, as_is = FALSE, do_round = TRUE, do_pos = TRUE, verbosity = 2, verbose = NULL, show_progress = NULL )
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 |
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 |
Corrected data as UMI counts
vst_out <- vst(pbmc, return_cell_attr = TRUE) umi_corrected <- correct(vst_out)
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