Something about Data format exporting and operation on matrix

[jefferyUstc]

Hi, I have gone through the paper and docs these days and great work! And I have some questions in my utilization on my own data analysis when using ArchR.

1. are there any utility interfaces to export h5ad or Seurat formats?
2. or instead, how can i get access to the matrixs in getAvailableMatrices(proj) . i hope i can get and set custom matrix. for example, set my own peakmatrix called from outside.

thank you so much!

[rcorces]

Thanks for using ArchR!

1. are there any utility interfaces to export h5ad or Seurat formats?

This is not explicitly possible in ArchR. If you find yourself wishing ArchR had some functionality that exists in other packages (for ex. Signac) feel free to open a Discussion thread for a feature request. ArchR does allow you to export data in some ways, mostly by creating SummarizedExperiments objects. This is illustrated at various points in the manual

2. how can i get access to the matrixs in getAvailableMatrices(proj) . i hope i can get and set custom matrix. for example, set my own peakmatrix called from outside.

For export of a matrix - I believe you are looking for the getMatrixFromProject() function. https://www.archrproject.com/reference/getMatrixFromProject.html
For import - you cannot import matrices yet but you can import your own peak set defined outside of ArchR and use this to create a peak matrix within ArchR. see addPeakSet() https://www.archrproject.com/reference/addPeakSet.html

If this answers your questions, feel free to mark this as "Answered"

[rcorces]

I would recommend familiarizing yourself with what a SummarizedExperiment object is and how to work with one.
https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

[brianpenghe]

what about exporting into a Seurat object?

[rcorces]

This isnt currently possible.

[brianpenghe]

I think one thing I can do is to save matrices from the ArchR object into matrix market formats and then read into other platforms