Matt Regner

@aina91 you change the dimension reduction slot as well as the clustering slot to store the original information from Seurat (writing to loom files seems to work well): ```` from...

Yes, DiagMultiKPlot() prints the optimal k values to the console. However, I am trying to implement MultiK in a pipeline context (non-interactively on a remote compute cluster). I will be...

Hi @siyao-liu I figured out how to store the optimal k as a new variable! I reconstruct the `tog` object for input into `findOptK()` using the following: ``` tog 1])...

No rush at all! The code above should suffice for my specific case. I appreciate your help. Thanks!

Hi @rcorces, While I have not yet had the chance to run this new implementation from the `dev_p2g` branch, I do have some follow up questions just to clarify and...

Thanks @rcorces, After revisiting this, I have been thinking that it may be more straightforward (from a user's standpoint and from a developer's standpoint) to implement the permutation strategy for...

Hi @AnjaliC4, PermPval represents the average null p-value across all permutations for each peak-to-gene link while PermFDR represents the actual "FDR adjusted p-value" derived empirically through permutation. Therefore, the PermPval...

Hi @jblich870, The large amount of zeros that you observing (relative to the other methods) could be due to a variety of factors (related to this specific PermFDR implementation and/or...

It is tough to comment on how optimal the PermFDR calculation is, but I would say it is still undergoing development here.