Tile Matrix from ArchR

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1

Can we use Tile Matrix from ArchR as input? Thanks!

2

Yes, any binary (or close-to-binary) matrix can be used as input. We don’t currently have a direct interface with ArchR projects, but you can extract the matrix using getMatrixFromProject.

We recommend that you filter the matrix to remove tiles that are very rarely observed (e.g detected in fewer than 1% of cells) since those generally increase the time to train the model without adding useful information.

3

Thanks for your quick answer and suggestions, Tal!

4

Hi Tal, I tried peakVI using tiled matrix from Arch and it worked. I have a question on pvi.differential_accessibility. For my dataset of 51319 × 27838, one versus all others have only <20 chromosome regions using is_da_fdr. I wonder if I can use a different criteria and select a bit more chromosome regions as da in one versus all others. Thanks, Tao

5

Hi Tao,
Glad it worked! For the differential accessibility, two things I would try:

  1. Try running the analysis in vanilla mode (mode="vanilla"). This basically set the minimal difference required to 0, which might help the analysis recover more significant results.
  2. If the “all” group in a “vs-all” comparison contains many cells that are highly similar to cells in the target group (for instance, a cluster that is very similar to the target cluster), this can reduce the ability of the analysis to accurately identify differential features. This If possible - try comparing against “all” except highly similar clusters.