Error: For now this only works downstream of slingshot

[RicardoMartins-Ferreira]

I am currently trying to apply your condiments pipeline for trajectory inferece in single cell data. However, I am getting some errors along the way, namely in the folowing steps:

• topologyTest()

Error in .local(sds, ...) :

For now this only works downstream of slingshot

• progressionTest()

Error in .local(pseudotime, ...) :

For now this only works downstream of slingshot

• evaluateK()

Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments.

Trying to figure it out what the problem was, I tried to ran your pipeline of the 1st example of the bioc2021trajectories workshop (“tgfb”). I get exactly the same errors as I did in my analysis.

Could you have any idea of what the problem is and how I can overcome it?

Thank you for the atention.

Ricardo Martins-Ferreira

[HectorRDB]

Hi @RicardoMartins-Ferreira Thanks for posting on Github. Can you tell me what versions of condiments and slingshot you are using? If you don;t have the latests version, please update and check if the issue persists. Best,

[HectorRDB]

Closing due to lack of activity. Feel free to reopen if issue persists.