Running Harmony with SingleCellExperiment object

[guillermoturiel]

Hi,

Recently I was trying to run Harmony with a SingleCellExperiment object and I got the following error:

Error in UseMethod("RunHarmony") : no applicable method for 'RunHarmony' applied to an object of class "c('SingleCellExperiment', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'RectangularData', 'Vector', 'Annotated', 'vector_OR_Vector')"

I have been using Harmony for a long time and I never had this problem before. I guess it is because I recently updated my R packages including Harmony because if I run again old scripts were Harmony was going fine it is not working anymore.

Could you please give me some feedback on this or any possible solution?

Thank you very much

[guillermoturiel]

Ok I found the problem. I first installed Harmony from CRAN and this version did not include S3method(RunHarmony,SingleCellExperiment)

I reinstalled the one from github and it includes it and everything worked again

[lcolladotor]

Hi! @madhavitippani and I ran into this issue and we also resolved it by installing the GitHub version of harmony. In particular, from sessioninfo::session_info() I have:

 harmony     * 0.1.0   2022-02-02 [1] Github (immunogenomics/harmony@c93de54)

Thanks for the report and solution @guillermoturiel =)

For others, you can use: remotes::install_github("immunogenomics/harmony").

[lcolladotor]

Hi,

I just wanted to check if you have plans on updating harmony on CRAN to resolve this issue.

I understand well that maintaining software is challenging and greatly appreciate any spare time you can devote to this.

Thanks! Leo