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ZhangLabGT / scMultiSim

A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
https://zhanglabgt.github.io/scMultiSim/
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Error - Object 'S1' not found #1

Closed vkorobeynyk closed 2 years ago

vkorobeynyk commented 2 years ago

Hi,

I am trying to go through the .Rmd vignettes and while running:

results <- SimulateTrueCounts(GRN_params, num_cells = 1000, unregulated_to_regulated_gene_ratio = 0.1, num_evfs = 500, diffEVF_fraction = 0.9, Sigma = 0.1, atac_effect = 0.5, beta = 0.4, d = 1, num_cycles = 2, cycle_length = 1.0, intrinsic_noise = 1, phyla = p3, randseed = 0, do_velocity = T, nregions_distribution = cumsum(c(0.1, 0.5, 0.4)))

I get an error:

Error in RNA_SEQ(evf_all, phyla, num_genes, num_cells, num_regulators, : object 'S1' not found

Any idea for a solution?

lhc70000 commented 2 years ago

Hi, sorry for the late reply! This repo contains a previous version of scMultiSim which links to an obsolete vignette, and I just fixed it. Please follow vignettes/sim_new.Rmd for the latest version.

We are still in the process of adding more tutorials and documentation. Feel free to reach out if you have any other questions!

vkorobeynyk commented 2 years ago

Hi, Thanks a lot for updating, I will try