Can't find the warped pseudotimes in the aligner object.

[scachero]

Hello,
We are trying to align two trajectories and we have succesfully created an aligner object that looks good. What we would like to do now is to retrieve the 'warped' pseudotimes for the cells from the query trajectory from the aligner object. Is there a way to do this?

Many thanks.

Sebastian

[dinithins]

Hello @scachero, Thanks for using Genes2Genes. G2G does not currently output a refined 'warped' pseudotime estimate. Instead, you can identify the warped regions of pseudotime from the 5-state alignment string (i.e., all V and W states that describe one-to-many/many-to-one matched time points between the respective reference and query pseudotime discretizations).

[scachero]

Thanks Dinithins!
We ended up writing a small function to aproximate the new pseudotimes based on the alignment.
Best,
Sebastian