Return Pearson or deviance residuals of regularized models
Return Pearson or deviance residuals of regularized models
get_residuals( vst_out, umi, residual_type = "pearson", res_clip_range = c(-sqrt(ncol(umi)), sqrt(ncol(umi))), min_variance = vst_out$arguments$min_variance, cell_attr = vst_out$cell_attr, bin_size = 256, verbosity = vst_out$arguments$verbosity, verbose = NULL, show_progress = NULL )
vst_out |
The output of a vst run |
umi |
The UMI count matrix that will be used |
residual_type |
What type of residuals to return; can be 'pearson' or 'deviance'; default is 'pearson' |
res_clip_range |
Numeric of length two specifying the min and max values the results will be clipped to; default is c(-sqrt(ncol(umi)), sqrt(ncol(umi))) |
min_variance |
Lower bound for the estimated variance for any gene in any cell when calculating pearson residual; default is vst_out$arguments$min_variance |
cell_attr |
Data frame of cell meta data |
bin_size |
Number of genes to put in each bin (to show progress) |
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 |
A matrix of residuals
vst_out <- vst(pbmc, return_cell_attr = TRUE) pearson_res <- get_residuals(vst_out, pbmc) deviance_res <- get_residuals(vst_out, pbmc, residual_type = 'deviance')
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