Bacth correct by other algorithm

[songlyzz]

Hi,
I found that harmony can not remove my batch effect, so I want to use other algorithm such as BBKNN, scVI, how can i implement it?

[Zepeng-Mu]

Hi, I had similar needs before and I wrote a wrapper function to use reducedMNN:
https://github.com/Zepeng-Mu/ArchRWrappers/blob/b4987d79d24ad47c3070e003354510767c2b4072/R/ArchR_helper.R#L44

Similarly, you can also run BBKNN, scVI or whatever you wish on the reduced dimension and then add the matrix back to ArchR obejct so you can do plotting and downstream analysis:
https://github.com/Zepeng-Mu/ArchRWrappers/blob/b4987d79d24ad47c3070e003354510767c2b4072/R/ArchR_helper.R#L125

Hope you find this helpful!

[songlyzz]

thanks very much, I run well with your code!