Please add the option to use clustering in colData

[david-priest]

Please add the option to use a custom clustering stored in the column data when the input data is an SCE with cluster codes.

[SamGG]

Hello, I think the best way is to use the package in a step-by-step way. In the code of generateClusters.R, the few final lines of code show how to add any clustering result to the d_se object. Best. https://github.com/lmweber/diffcyt/blob/39348fd4ebba6a2ca5c38325e587d5c9047f3fda/R/3_generateClusters.R#L168-L172

[SamGG]

I think I mis-read your question. I thought you have carried out a table of counts per sample and per cluster.

If the input of the diffcyt wrapper/function is an SCE object, you can set the clustering_to_use argument to inform about the clustering column.

Unfortunately, I think it will currently fail as reported in Cell populations in topTable() wrong