Error in get_residuals(), 'log_umi' not found

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

GNU General Public License v3.0

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Open frederikziebell opened 3 years ago

frederikziebell commented 3 years ago

Running

vst_out <- vst(pbmc)
get_residuals(vst_out, pbmc)

gives Error in eval(predvars, data, env) : object 'log_umi' not found on sctransform version 0.3.

ChristophH commented 3 years ago

Thank you for reporting this. Yes, the example is broken - I will fix that. It should be

vst_out <- vst(pbmc, return_cell_attr = TRUE)
pearson_res <- get_residuals(vst_out, pbmc)