no applicable method for "'RunHarmony'" applied to an object of class "seurat"

[yingyonghui]

Hi all, I'm just wondering whether harmony is compatible with Seurat v2. I run vignettes exactly following the tutorial here, only to end up with the error " no applicable method for "'RunHarmony'" applied to an object of class "seurat" ". So anyone has the same questions? Any suggestions would be appreciated!

Here are the main packages I used: [1] harmony_1.0 Rcpp_1.0.1 magrittr_1.5 Seurat_2.3.4 Matrix_1.2-17 [6] cowplot_0.9.4 ggplot2_3.1.1

Best, Yonghui

[L1H0n9Jun]

> class(seurat_v2_object)
'seurat'

I found that in commit 512f6b24d0d2b8c913c4fa068d6a73c35e73a50d, this was removed from NAMESPACE as:

- S3method(RunHarmony,seurat)

Don't know the reason. But if you insist to use this wrapper in Seurat v2, you could install the commit 818123eff65eca65bd96ee8ad2b56d58002ab290 as:

remotes::install_github("immunogenomics/harmony@818123eff65eca65bd96ee8ad2b56d58002ab290")

This version, which includes seurat v2 class seurat in NAMESPACE and the wrapper function, could work in your environment. Don't forget to remove your current harmony first.

[ilyakorsunsky]

Dear @L1H0n9Jun and @yingyonghui,

That's right, we removed this support during one of the pushes. Please let me know if you still need to run harmony with Seurat v2 and I will look into re-introducing the wrapper.

Best, Ilya