Bug: dims.use is not working

[andreaskapou]

Hi,

Just to note that there is a bug in your code and the dims.use parameter is ignored inside the code and never subsets the embedding matrix. This was brought as an issue earlier ( #82 ).

The issue is that you never subset the embedding matrix you extract with the dims.use parameter. You just need to add this line in the RunHarmony.R file (in all functions for Seurat, SCE etc):

embedding <- embedding[, dims.use]

for instance after line https://github.com/immunogenomics/harmony/blob/master/R/RunHarmony.R#L120 for the Seurat specific function.

Best, Andreas