PCA/Clustering with ChIP-Data but functional not genomic ranges

Question

[schmau]

Hi,

there are a few tools to do a PCA with BED-Files and the corresponding genomic ranges, but has anyone some experience with doing a PCA on functional features? Like: Intergenic/Intron/Exon/..., GC-content, other ChIP sets (Histones, TF), etc. of the ChIP-data? The feature used in for example an UpSet-Plot.

Thanks in advance