How to merge ArchR projects

[ShijingZHANG]

Hello!

I have two samples, and for each sample there are three replicates. For sample A, there are a1, a2, a3; for sample B, there are b1, b2, b3. For each replicates, I create a ArchR project. Now I want to compare the two samples to get differential peaks, how can I merge the six ArchR projects to form one ArchR project, which can group by sample? (Let a1+a2+a3 compare with b1+b2+b3)

Thank you!

Best regards,
Shijing

[rcorces]

As indicated when you tried to open this issue, Issues are not for usage questions. This belongs in Discussions and I have moved it there.

[rcorces]

Your question indicates some confusion about ArchR basics. Please read the manual in full and go through the tutorial.

An ArchRProject consists of multiple arrow files. Each arrow file corresponds to a different sample. You cannot compare across ArchRProjects nor can you merge ArchRProjects. You should create a single ArchRProject containing all of the samples you wish to compare.

[rcorces]

you cant add data.frames to an ArchRProject per se - you will have to update the cellColData with additional annotation columns

[brianpenghe]

Yes it worked! Thanks!

[Zepeng-Mu]

I'm wondering whether I can run ArchRProject using arrow files A and B created under projects A and B, respectively.
ArchRProject accepts more than one arrow files, but it does not seem to work in this case, as there is an error message when I tried to subset the merged project.

[rcorces]

The problem is that ArrowFiles have a lot of information that is expected based on values stored in the ArchRProject. So it would be extremely easy to run into incompatibilities doing this. This isnt really a use case that is supported by ArchR.

[Zepeng-Mu]

OK, thanks. I should start with fragment files to make arrow files then.