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BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data
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Question about CCI distance #263

Closed Knight1995 closed 3 months ago

Knight1995 commented 7 months ago

Thanks for great jobs. I have some questions about the distance in the st.tl.cci.run function.The tutorial annotation is as follows: distance=None, # None defaults to spot+immediate neighbors; distance=0 for within-spot mode. My questions are:

  1. If I want to test all the spots in a silde, there is no distance restriction.What should I set the papameter to? 10,000 or other?
  2. If I set the distance parameter to 10,000, which is larger than the slide,may it affect my CCC result?
  3. Is the result of distance 10,000 and 100,000 different? Thanks for your help!