Option GRN is required but not presented.

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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Option GRN is required but not presented. #2

Closed ivanovaos closed 1 year ago

ivanovaos commented 1 year ago

Hello,

Thanks for the great tool! I am testing it out, and as far as I understand GRN input is optional? However, when I am trying to run with options

options_ = list(
  rand.seed = 0,
  num.cells = 1000,
  num.cifs = 500,
  tree = Phyla5(),
  diff.cif.fraction = 0.8,
  do.velocity = T,
  intrinsic.noise = 1
  # debug = T
)

I get "Error in OP(GRN) : Option GRN is required but not presented." Is this supposed to be this way?

Thank you!

lhc70000 commented 1 year ago

Hi, please set the GRN to NA:

options_ = list(
  rand.seed = 0,
  num.cells = 1000,
  num.cifs = 500,
  tree = Phyla5(),
  GRN = NA,
  diff.cif.fraction = 0.8,
  do.velocity = T,
  intrinsic.noise = 1
)

I also found another problem and just pushed the updated code, so please pull/clone the repo again before running it (sorry for that; we are still preparing the code for the release). Please let me know if you have other questions. Thanks!