object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance

[shuaizh117]

object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance

[MikeDMorgan]

First, if you kill an Rsession mid-execution it will give often an error around where the code was executing at the time - so this error message is irrelvant.

Second, switch to using refinement_scheme="graph" in makeNhoods and fdr.weighting="graph-overlap" in testNhoods - these supercede the old calcNhoodDistances approach to refining nhoods.

Finally, please refer to the GitHub readme about posting issues, i.e. sessionInfo, etc.

[shuaizh117]

First, if you kill an Rsession mid-execution it will give often an error around where the code was executing at the time - so this error message is irrelvant.

Second, switch to using refinement_scheme="graph" in makeNhoods and fdr.weighting="graph-overlap" in testNhoods - these supercede the old calcNhoodDistances approach to refining nhoods.

Finally, please refer to the GitHub readme about posting issues, i.e. sessionInfo, etc.

I didn't realize it would take 1h-ish for calcNhoodDistance to complete the job (~ 70K cells). Thank you for your comments and will follow what you advised.