Error in run.CSIDE.replicates: 'object RCTD_controls not found'

[krademaker]

Hello Dylan,

Running the run.CSIDE.replicates function with de_mode = 'general' will throw the following error:

run.CSIDE.replicates: running CSIDE for replicate 1

Error in rownames(RCTD_controls@RCTD.reps[[i]]@results$weights): object 'RCTD_controls' not found
Traceback:

1. run.CSIDE.replicates(Polioudakis_broad.RCTD.subset, cell_types = all_cell_types, 
 .     X.replicates = X.replicates, gene_threshold = 5e-05, cell_type_threshold = 10, 
 .     fdr = 0.01, weight_threshold = 0.5, doublet_mode = FALSE, 
 .     de_mode = "general")
2. setdiff(rownames(X), rownames(RCTD_controls@RCTD.reps[[i]]@results$weights))
3. as.vector(y)
4. rownames(RCTD_controls@RCTD.reps[[i]]@results$weights)

The error originates at this line, where the RCTD.replicates object that is passed as parameter to the function is being called as RCTD_controls instead, which doesn't exist.

Best,
Koen

[Dillon214]

Getting this problem as well. I imagine it is a typo and meant to be the variable RCTD.replicates? I'm not sure...
Did you determine a good workaround for this, by any chance?

[krademaker]

@Dillon214 For now I simply replaced the line RCTD_controls@RCTD.reps with RCTD.replicates@RCTD.reps