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Error when running run.CSIDE.replicates, doublet_mode not found in myRCTD@config #177
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Hello, I came across the same issue with the |
Hi DanielZucha, rpisalive |
Hello @glzhang90095 , rather than modifying the original code, I simply added a slot to create myRCTD@config$doublet_mode == 'full' so that myRCTD@config$doublet_mode == "full" could be found when the function aggregate_cell_types is calling it. I had multiple samples so I added myRCTD@config$doublet_mode == 'full' for each sample. By doing that, I did not see the error again. |
@rpisalive Thanks for your quick response! [email protected][1][[1]]@config$doublet_mode = 'full'
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Hello and sorry for the late response. I confirm that I implemented solution identical as outlined by @rpisalive. Happy coding! |
Hello,
I ran run.RCTD.replicates on multiple replicates (visium data) with doublet_mode 'full' and there is a RCTDmode 'full' stored in myRCTD@config. When I further ran run.CSIDE.replicates, error message shows up:
run.CSIDE.replicates: running CSIDE for replicate 1
**Error in if (myRCTD@config$doublet_mode == "multi") {: argument is of length zero
Traceback:
. cell_type_threshold = 2, doublet_mode = F, weight_threshold = 0.95,
. population_de = T)
. cell_types = cell_types, cell_type_threshold = cell_type_threshold,
. gene_threshold = gene_threshold, doublet_mode = doublet_mode,
. weight_threshold = weight_threshold, sigma_gene = sigma_gene,
. PRECISION.THRESHOLD = PRECISION.THRESHOLD, test_genes_sig = test_genes_sig_individual,
. cell_types_present = cell_types_present, fdr = fdr, log_fc_thresh = log_fc_thresh,
. test_error = test_error)
It looks like myRCTD@config$doublet_mode, which does not exist, is being called by the function aggregate_cell_types: link. As there is no doublet_mode in the config, the error happened. I am not sure if I misunderstood something but run.CSIDE.replicates worked when I added doublet_mode 'full' to the config.
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