Problem getting matrixes? "$ operator not defined"?

[mfrenkel16]

Hi,

I am trying to get the matrixes (e.g. TileMatrix, GeneScoreMatrix etc.) from an arrow file/project for custom analysis outside of ArchR. All of the analysis within ArchR works and I'm able to retrieve the matrixes with either getMatrixFromArrow or getMatrixFromProject . However, I can't find a way to access the actual count data within. For instance, the command test3@assays$GeneScoreMatrix results in the error "$ operator not defined for this S4 class" even though tabbing to complete after $ works suggesting that is a way to access the matrix. This error occurs regardless of which matrix I try retrieving and regardless of whether I get it from the arrow file or the project.

Am I going about this wrong or can I access the actual data within these matrixes in some other way?

Thanks!
Max

[mfrenkel16]

Solved (of course 15 min after posting, despite >1 day of troubleshooting).

For others in a similar boat, here's the way to access the matrix: test3@assays@data$GeneScoreMatrix (not test3@assays$GeneScoreMatrix even though tab to complete would suggest that's a way to access it)

[rcorces]

just to add to this, typically this is done using assays(test3)

[mfrenkel16]

Thank you! This is obviously a case of me not knowing the structure of these files well enough so I appreciate the follow up.