| correct_counts {sctransform} | R Documentation |
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.
correct_counts(x, umi, cell_attr = x$cell_attr, show_progress = TRUE)
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 |
show_progress |
Whether to print progress bar |
Corrected data as UMI counts
vst_out <- vst(pbmc, return_cell_attr = TRUE) umi_corrected <- correct_counts(vst_out, pbmc)